Starting phenix.real_space_refine on Mon Mar 11 01:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9t_37381/03_2024/8w9t_37381.pdb" } resolution = 2.6 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= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 Na 2 4.78 5 C 4324 2.51 5 N 1054 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.65 Number of scatterers: 6574 At special positions: 0 Unit cell: (101.37, 84.63, 86.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 Na 2 11.00 O 1148 8.00 N 1054 7.00 C 4324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.34 Conformation dependent library (CDL) restraints added in 1.3 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.564A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 removed outlier: 3.757A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.528A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 removed outlier: 3.525A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 65 removed outlier: 3.563A pdb=" N ALA B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.756A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.530A pdb=" N LEU B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.526A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1296 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: 1.82 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1365 1.33 - 1.45: 1476 1.45 - 1.57: 3803 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" CA ARG A 367 " pdb=" CB ARG A 367 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.27e-02 6.20e+03 4.06e+00 bond pdb=" CA ARG B 367 " pdb=" CB ARG B 367 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.85e+00 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.23e-02 6.61e+03 3.47e+00 bond pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 1.544 1.520 0.023 1.30e-02 5.92e+03 3.18e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.95: 161 105.95 - 112.96: 3810 112.96 - 119.97: 2210 119.97 - 126.98: 2881 126.98 - 133.99: 72 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N LEU A 87 " pdb=" CA LEU A 87 " pdb=" C LEU A 87 " ideal model delta sigma weight residual 111.28 115.08 -3.80 1.09e+00 8.42e-01 1.22e+01 angle pdb=" N LEU B 87 " pdb=" CA LEU B 87 " pdb=" C LEU B 87 " ideal model delta sigma weight residual 111.28 115.01 -3.73 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N ILE A 374 " pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 112.32 108.44 3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 112.04 107.41 4.63 1.44e+00 4.82e-01 1.04e+01 angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 112.04 107.91 4.13 1.44e+00 4.82e-01 8.25e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 3572 15.72 - 31.43: 304 31.43 - 47.15: 72 47.15 - 62.87: 6 62.87 - 78.59: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ARG A 367 " pdb=" C ARG A 367 " pdb=" N HIS A 368 " pdb=" CA HIS A 368 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG B 367 " pdb=" C ARG B 367 " pdb=" N HIS B 368 " pdb=" CA HIS B 368 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 780 0.041 - 0.081: 264 0.081 - 0.122: 56 0.122 - 0.163: 7 0.163 - 0.203: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 88 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C THR A 88 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 88 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 89 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C GLU B 252 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.03e+00 pdb=" C GLU A 252 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.014 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 6554 3.21 - 3.78: 10886 3.78 - 4.34: 15511 4.34 - 4.90: 24867 Nonbonded interactions: 57901 Sorted by model distance: nonbonded pdb=" O GLN B 424 " pdb=" OG1 THR B 527 " model vdw 2.090 2.440 nonbonded pdb=" O GLN A 424 " pdb=" OG1 THR A 527 " model vdw 2.091 2.440 nonbonded pdb=" NH2 ARG A 367 " pdb=" O PRO A 394 " model vdw 2.189 2.520 nonbonded pdb=" NH2 ARG B 367 " pdb=" O PRO B 394 " model vdw 2.189 2.520 nonbonded pdb=" O GLY B 91 " pdb=" O HOH B 801 " model vdw 2.257 2.440 ... (remaining 57896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 2.770 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.130 Find NCS groups from input model: 0.330 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6718 Z= 0.285 Angle : 0.601 6.685 9134 Z= 0.333 Chirality : 0.043 0.203 1110 Planarity : 0.005 0.041 1108 Dihedral : 12.297 78.585 2370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 840 helix: -0.90 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS B 368 PHE 0.011 0.001 PHE A 361 TYR 0.015 0.002 TYR B 50 ARG 0.004 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.869 Fit side-chains REVERT: A 69 ASN cc_start: 0.7256 (t0) cc_final: 0.7047 (t0) REVERT: A 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6743 (mm) REVERT: A 447 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6616 (ttp-110) REVERT: B 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6742 (mm) REVERT: B 447 ARG cc_start: 0.6940 (mtp85) cc_final: 0.6620 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.2319 time to fit residues: 132.3175 Evaluate side-chains 75 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 260 ASN A 270 GLN A 309 HIS A 312 ASN A 358 ASN A 368 HIS A 484 HIS B 69 ASN B 253 ASN B 260 ASN B 270 GLN B 309 HIS B 312 ASN B 358 ASN B 368 HIS B 484 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6718 Z= 0.178 Angle : 0.510 5.793 9134 Z= 0.268 Chirality : 0.039 0.145 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.341 19.162 896 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 10.00 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.28), residues: 840 helix: 0.95 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 502 HIS 0.007 0.002 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.015 0.002 TYR A 50 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.876 Fit side-chains REVERT: A 447 ARG cc_start: 0.6741 (mtp85) cc_final: 0.6383 (ttp-110) REVERT: B 447 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6391 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 103 average time/residue: 0.9974 time to fit residues: 109.3559 Evaluate side-chains 85 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6718 Z= 0.230 Angle : 0.543 7.035 9134 Z= 0.282 Chirality : 0.041 0.142 1110 Planarity : 0.004 0.042 1108 Dihedral : 4.451 21.534 896 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 11.87 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 840 helix: 1.51 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.27 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 287 HIS 0.006 0.002 HIS B 487 PHE 0.011 0.001 PHE A 463 TYR 0.014 0.002 TYR A 76 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.872 Fit side-chains REVERT: A 256 ILE cc_start: 0.8321 (tt) cc_final: 0.8112 (tt) REVERT: A 300 LEU cc_start: 0.6826 (mt) cc_final: 0.6617 (mm) REVERT: B 256 ILE cc_start: 0.8325 (tt) cc_final: 0.8115 (tt) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 1.2979 time to fit residues: 136.7351 Evaluate side-chains 93 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0270 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6718 Z= 0.128 Angle : 0.464 6.034 9134 Z= 0.239 Chirality : 0.037 0.139 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.908 15.285 896 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.40 % Allowed : 13.47 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.29), residues: 840 helix: 2.27 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 531 HIS 0.005 0.001 HIS A 487 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.001 TYR B 50 ARG 0.001 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.965 Fit side-chains REVERT: A 447 ARG cc_start: 0.6636 (mtp85) cc_final: 0.6423 (ttp-110) REVERT: B 447 ARG cc_start: 0.6637 (mtp85) cc_final: 0.6425 (ttp-110) REVERT: B 529 LYS cc_start: 0.6215 (ptmm) cc_final: 0.5918 (pttp) outliers start: 18 outliers final: 6 residues processed: 104 average time/residue: 1.0383 time to fit residues: 114.9726 Evaluate side-chains 89 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6718 Z= 0.282 Angle : 0.574 7.289 9134 Z= 0.297 Chirality : 0.042 0.158 1110 Planarity : 0.004 0.043 1108 Dihedral : 4.447 20.629 896 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.80 % Allowed : 14.53 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 840 helix: 1.99 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.08 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 45 HIS 0.007 0.002 HIS A 368 PHE 0.013 0.002 PHE B 463 TYR 0.013 0.002 TYR A 76 ARG 0.003 0.001 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.834 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 97 average time/residue: 1.1232 time to fit residues: 115.6295 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6718 Z= 0.156 Angle : 0.490 6.482 9134 Z= 0.252 Chirality : 0.039 0.130 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.060 15.999 896 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.13 % Allowed : 15.87 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 840 helix: 2.39 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.02 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 531 HIS 0.005 0.001 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.014 0.002 TYR B 50 ARG 0.001 0.000 ARG A 519 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.817 Fit side-chains REVERT: A 256 ILE cc_start: 0.8268 (tt) cc_final: 0.8044 (tt) REVERT: A 447 ARG cc_start: 0.6614 (mtp85) cc_final: 0.6324 (ttp-110) REVERT: B 256 ILE cc_start: 0.8277 (tt) cc_final: 0.8048 (tt) REVERT: B 447 ARG cc_start: 0.6616 (mtp85) cc_final: 0.6325 (ttp-110) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 1.0597 time to fit residues: 104.7145 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.0170 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6718 Z= 0.176 Angle : 0.505 6.620 9134 Z= 0.259 Chirality : 0.039 0.129 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.115 17.166 896 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.13 % Allowed : 16.53 % Favored : 81.33 % 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: 2.13 (0.29), residues: 840 helix: 2.42 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 287 HIS 0.006 0.002 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.014 0.002 TYR A 76 ARG 0.002 0.000 ARG A 519 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.914 Fit side-chains REVERT: A 256 ILE cc_start: 0.8287 (tt) cc_final: 0.8036 (tt) REVERT: A 447 ARG cc_start: 0.6650 (mtp85) cc_final: 0.6345 (ttp-110) REVERT: A 529 LYS cc_start: 0.6430 (ptmm) cc_final: 0.6034 (pttp) REVERT: B 256 ILE cc_start: 0.8287 (tt) cc_final: 0.8028 (tt) REVERT: B 447 ARG cc_start: 0.6653 (mtp85) cc_final: 0.6345 (ttp-110) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 1.1259 time to fit residues: 116.9134 Evaluate side-chains 97 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6718 Z= 0.140 Angle : 0.485 6.256 9134 Z= 0.247 Chirality : 0.039 0.128 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.892 14.193 896 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.40 % Allowed : 16.27 % Favored : 81.33 % 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: 2.41 (0.29), residues: 840 helix: 2.63 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 531 HIS 0.005 0.001 HIS B 368 PHE 0.011 0.001 PHE B 198 TYR 0.014 0.002 TYR B 50 ARG 0.001 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.696 Fit side-chains REVERT: A 57 LEU cc_start: 0.8099 (mt) cc_final: 0.7500 (tp) REVERT: A 256 ILE cc_start: 0.8249 (tt) cc_final: 0.8017 (tt) REVERT: A 307 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6042 (mm-30) REVERT: A 447 ARG cc_start: 0.6696 (mtp85) cc_final: 0.6466 (ttp-110) REVERT: A 529 LYS cc_start: 0.6234 (ptmm) cc_final: 0.5901 (pttt) REVERT: B 57 LEU cc_start: 0.8099 (mt) cc_final: 0.7497 (tp) REVERT: B 256 ILE cc_start: 0.8262 (tt) cc_final: 0.8009 (tt) REVERT: B 447 ARG cc_start: 0.6697 (mtp85) cc_final: 0.6468 (ttp-110) REVERT: B 529 LYS cc_start: 0.6288 (ptmm) cc_final: 0.5949 (pttt) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 1.0355 time to fit residues: 109.9415 Evaluate side-chains 103 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 244 ASN B 69 ASN B 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6718 Z= 0.126 Angle : 0.469 6.036 9134 Z= 0.240 Chirality : 0.038 0.120 1110 Planarity : 0.004 0.039 1108 Dihedral : 3.706 13.070 896 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.40 % Allowed : 16.67 % Favored : 80.93 % 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: 2.67 (0.29), residues: 840 helix: 2.85 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 531 HIS 0.004 0.001 HIS B 487 PHE 0.011 0.001 PHE A 198 TYR 0.013 0.001 TYR A 50 ARG 0.001 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.791 Fit side-chains REVERT: A 57 LEU cc_start: 0.8123 (mt) cc_final: 0.7543 (tp) REVERT: A 256 ILE cc_start: 0.8243 (tt) cc_final: 0.8003 (tt) REVERT: A 307 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6020 (mm-30) REVERT: A 447 ARG cc_start: 0.6778 (mtp85) cc_final: 0.6558 (ttp-110) REVERT: A 529 LYS cc_start: 0.6166 (ptmm) cc_final: 0.5878 (pttt) REVERT: B 57 LEU cc_start: 0.8122 (mt) cc_final: 0.7539 (tp) REVERT: B 256 ILE cc_start: 0.8236 (tt) cc_final: 0.7996 (tt) REVERT: B 447 ARG cc_start: 0.6777 (mtp85) cc_final: 0.6559 (ttp-110) REVERT: B 529 LYS cc_start: 0.6171 (ptmm) cc_final: 0.5860 (pttt) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.9910 time to fit residues: 110.6061 Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6718 Z= 0.189 Angle : 0.522 6.626 9134 Z= 0.267 Chirality : 0.040 0.133 1110 Planarity : 0.004 0.040 1108 Dihedral : 4.064 17.726 896 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 16.80 % Favored : 81.07 % 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: 2.28 (0.29), residues: 840 helix: 2.54 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.006 0.002 HIS B 368 PHE 0.010 0.001 PHE A 463 TYR 0.015 0.002 TYR B 76 ARG 0.002 0.000 ARG A 519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.749 Fit side-chains REVERT: A 256 ILE cc_start: 0.8232 (tt) cc_final: 0.8023 (tt) REVERT: A 307 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5986 (mm-30) REVERT: A 447 ARG cc_start: 0.6731 (mtp85) cc_final: 0.6442 (ttp-110) REVERT: B 256 ILE cc_start: 0.8256 (tt) cc_final: 0.8022 (tt) REVERT: B 447 ARG cc_start: 0.6733 (mtp85) cc_final: 0.6441 (ttp-110) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 1.0119 time to fit residues: 107.7551 Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130431 restraints weight = 7779.616| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.25 r_work: 0.3367 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.134 Angle : 0.479 6.533 9134 Z= 0.243 Chirality : 0.038 0.128 1110 Planarity : 0.004 0.039 1108 Dihedral : 3.797 14.000 896 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.33 % 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: 2.58 (0.29), residues: 840 helix: 2.79 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 531 HIS 0.004 0.001 HIS B 487 PHE 0.011 0.001 PHE A 198 TYR 0.013 0.001 TYR A 50 ARG 0.001 0.000 ARG B 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.48 seconds wall clock time: 45 minutes 39.95 seconds (2739.95 seconds total)