Starting phenix.real_space_refine on Mon Sep 23 16:21:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/09_2024/5ly6_4118.cif" } resolution = 4.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic. 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 7 5.16 5 C 2350 2.51 5 N 633 2.21 5 O 735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3725 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3725 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 452} Time building chain proxies: 3.21, per 1000 atoms: 0.86 Number of scatterers: 3725 At special positions: 0 Unit cell: (85.4, 78.4, 127.4, 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 7 16.00 O 735 8.00 N 633 7.00 C 2350 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 12.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.880A pdb=" N ARG B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.669A pdb=" N ARG B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=A, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.614A pdb=" N ARG B 31 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 44 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 43 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 357 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 45 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 355 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 353 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'B' and resid 147 through 149 removed outlier: 3.577A pdb=" N GLU B 258 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 191 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 250 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 197 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 152 through 165 Processing sheet with id=E, first strand: chain 'B' and resid 235 through 237 removed outlier: 4.147A pdb=" N TYR B 331 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 345 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 261 through 264 Processing sheet with id=G, first strand: chain 'B' and resid 408 through 413 removed outlier: 4.183A pdb=" N ARG B 451 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 364 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 368 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 457 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.910A pdb=" N VAL B 372 " --> pdb=" O CYS B 428 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'B' and resid 382 through 384 Processing sheet with id=J, first strand: chain 'B' and resid 440 through 442 removed outlier: 4.087A pdb=" N TYR B 440 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 425 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 442 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 423 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 419 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 380 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 421 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=J 101 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1239 1.34 - 1.46: 424 1.46 - 1.57: 2121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 3798 Sorted by residual: bond pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 1.332 1.597 -0.265 1.29e-02 6.01e+03 4.22e+02 bond pdb=" N PRO B 413 " pdb=" CD PRO B 413 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" C ILE B 412 " pdb=" N PRO B 413 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.86e+00 bond pdb=" CA ALA B 64 " pdb=" CB ALA B 64 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.55e-02 4.16e+03 3.44e+00 bond pdb=" C HIS B 324 " pdb=" O HIS B 324 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.58e+00 ... (remaining 3793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 5147 5.44 - 10.88: 9 10.88 - 16.33: 4 16.33 - 21.77: 0 21.77 - 27.21: 4 Bond angle restraints: 5164 Sorted by residual: angle pdb=" O THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 123.24 111.38 11.86 1.23e+00 6.61e-01 9.30e+01 angle pdb=" CA THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 115.58 126.98 -11.40 1.48e+00 4.57e-01 5.93e+01 angle pdb=" C LEU B 39 " pdb=" N PRO B 40 " pdb=" CD PRO B 40 " ideal model delta sigma weight residual 125.00 97.79 27.21 4.10e+00 5.95e-02 4.40e+01 angle pdb=" C ASP B 117 " pdb=" N PRO B 118 " pdb=" CD PRO B 118 " ideal model delta sigma weight residual 125.00 99.67 25.33 4.10e+00 5.95e-02 3.82e+01 angle pdb=" C ALA B 273 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 125.00 102.20 22.80 4.10e+00 5.95e-02 3.09e+01 ... (remaining 5159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 1777 17.28 - 34.56: 264 34.56 - 51.85: 163 51.85 - 69.13: 64 69.13 - 86.41: 18 Dihedral angle restraints: 2286 sinusoidal: 905 harmonic: 1381 Sorted by residual: dihedral pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " pdb=" CG ASN B 30 " pdb=" OD1 ASN B 30 " ideal model delta sinusoidal sigma weight residual -90.00 -161.80 71.80 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -159.76 69.76 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.95 44.05 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 498 0.033 - 0.067: 17 0.067 - 0.100: 65 0.100 - 0.133: 4 0.133 - 0.167: 6 Chirality restraints: 590 Sorted by residual: chirality pdb=" CB THR B 63 " pdb=" CA THR B 63 " pdb=" OG1 THR B 63 " pdb=" CG2 THR B 63 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CB THR B 65 " pdb=" CA THR B 65 " pdb=" OG1 THR B 65 " pdb=" CG2 THR B 65 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ALA B 12 " pdb=" N ALA B 12 " pdb=" C ALA B 12 " pdb=" CB ALA B 12 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 587 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 39 " -0.120 5.00e-02 4.00e+02 1.91e-01 5.81e+01 pdb=" N PRO B 40 " 0.329 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 117 " -0.116 5.00e-02 4.00e+02 1.84e-01 5.42e+01 pdb=" N PRO B 118 " 0.318 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 273 " 0.111 5.00e-02 4.00e+02 1.76e-01 4.93e+01 pdb=" N PRO B 274 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " 0.084 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 20 2.20 - 2.88: 1637 2.88 - 3.55: 4768 3.55 - 4.23: 7738 4.23 - 4.90: 12540 Nonbonded interactions: 26703 Sorted by model distance: nonbonded pdb=" CG1 VAL B 78 " pdb=" CD PRO B 233 " model vdw 1.526 3.860 nonbonded pdb=" OD1 ASP B 295 " pdb=" ND1 HIS B 324 " model vdw 1.808 3.120 nonbonded pdb=" CG2 VAL B 302 " pdb=" CD1 LEU B 313 " model vdw 1.854 3.880 nonbonded pdb=" N LEU B 76 " pdb=" O VAL B 235 " model vdw 1.876 3.120 nonbonded pdb=" CG1 VAL B 78 " pdb=" CG PRO B 233 " model vdw 1.894 3.860 ... (remaining 26698 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 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 : 0.006 0.265 3798 Z= 0.393 Angle : 1.237 27.209 5164 Z= 0.692 Chirality : 0.034 0.167 590 Planarity : 0.018 0.191 668 Dihedral : 24.278 86.412 1394 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 94.62 Ramachandran Plot: Outliers : 4.90 % Allowed : 20.90 % Favored : 74.20 % Rotamer: Outliers : 36.32 % Allowed : 24.94 % Favored : 38.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -5.32 (0.32), residues: 469 helix: -1.20 (0.61), residues: 63 sheet: -2.85 (0.35), residues: 189 loop : -4.99 (0.27), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 436 HIS 0.000 0.000 HIS B 135 PHE 0.001 0.000 PHE B 9 TYR 0.003 0.000 TYR B 15 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 64 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8383 (t) REVERT: B 106 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8530 (pt) REVERT: B 151 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5919 (tp30) REVERT: B 194 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7211 (t0) REVERT: B 236 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (p90) REVERT: B 288 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.5882 (mmtt) REVERT: B 349 ASP cc_start: 0.7404 (p0) cc_final: 0.7117 (p0) REVERT: B 448 VAL cc_start: 0.4786 (OUTLIER) cc_final: 0.4353 (p) outliers start: 150 outliers final: 33 residues processed: 192 average time/residue: 0.2032 time to fit residues: 45.2482 Evaluate side-chains 87 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 47 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 245 GLN B 324 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 3798 Z= 0.344 Angle : 0.858 8.938 5164 Z= 0.448 Chirality : 0.049 0.240 590 Planarity : 0.009 0.105 668 Dihedral : 5.479 26.234 509 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.51 % Favored : 87.63 % Rotamer: Outliers : 0.48 % Allowed : 5.57 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -4.14 (0.35), residues: 469 helix: -0.58 (0.68), residues: 61 sheet: -2.00 (0.37), residues: 183 loop : -4.13 (0.32), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 134 HIS 0.007 0.002 HIS B 156 PHE 0.020 0.002 PHE B 335 TYR 0.026 0.003 TYR B 199 ARG 0.005 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.1944 time to fit residues: 9.8894 Evaluate side-chains 24 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 overall best weight: 3.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3798 Z= 0.266 Angle : 0.695 7.488 5164 Z= 0.364 Chirality : 0.045 0.213 590 Planarity : 0.008 0.090 668 Dihedral : 4.979 29.914 509 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.85 % Allowed : 10.23 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.58 (0.37), residues: 469 helix: 0.03 (0.72), residues: 61 sheet: -1.75 (0.35), residues: 213 loop : -3.91 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.009 0.001 HIS B 135 PHE 0.008 0.001 PHE B 320 TYR 0.025 0.002 TYR B 15 ARG 0.006 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7842 (pt) cc_final: 0.7308 (pt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1928 time to fit residues: 8.1291 Evaluate side-chains 21 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.9280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3798 Z= 0.304 Angle : 0.744 16.173 5164 Z= 0.374 Chirality : 0.045 0.290 590 Planarity : 0.007 0.095 668 Dihedral : 5.194 29.157 509 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.09 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.43 (0.36), residues: 469 helix: -0.76 (0.61), residues: 73 sheet: -1.65 (0.35), residues: 215 loop : -3.63 (0.35), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 278 HIS 0.007 0.002 HIS B 135 PHE 0.013 0.002 PHE B 335 TYR 0.021 0.003 TYR B 15 ARG 0.009 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8026 (pt) cc_final: 0.7623 (pt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1739 time to fit residues: 6.4162 Evaluate side-chains 19 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 1.0296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 3798 Z= 0.382 Angle : 0.810 9.658 5164 Z= 0.418 Chirality : 0.046 0.194 590 Planarity : 0.007 0.106 668 Dihedral : 5.755 21.250 509 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.30 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.31 (0.37), residues: 469 helix: -1.21 (0.63), residues: 65 sheet: -1.55 (0.33), residues: 235 loop : -3.38 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 278 HIS 0.013 0.003 HIS B 135 PHE 0.022 0.003 PHE B 335 TYR 0.023 0.003 TYR B 71 ARG 0.007 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8114 (pt) cc_final: 0.7577 (pt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2208 time to fit residues: 6.2401 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 1.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3798 Z= 0.261 Angle : 0.674 7.547 5164 Z= 0.343 Chirality : 0.044 0.155 590 Planarity : 0.007 0.119 668 Dihedral : 5.661 30.628 509 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.59 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 5.88 % 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: -3.00 (0.37), residues: 469 helix: -0.89 (0.67), residues: 59 sheet: -1.27 (0.34), residues: 211 loop : -3.12 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 134 HIS 0.009 0.002 HIS B 135 PHE 0.013 0.002 PHE B 43 TYR 0.018 0.002 TYR B 150 ARG 0.010 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8005 (pt) cc_final: 0.7596 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2258 time to fit residues: 7.1152 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 1.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3798 Z= 0.278 Angle : 0.686 7.608 5164 Z= 0.350 Chirality : 0.043 0.145 590 Planarity : 0.007 0.129 668 Dihedral : 5.623 25.859 509 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.30 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.36), residues: 469 helix: -0.91 (0.66), residues: 59 sheet: -1.25 (0.34), residues: 213 loop : -3.10 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.008 0.002 HIS B 135 PHE 0.013 0.002 PHE B 43 TYR 0.017 0.002 TYR B 371 ARG 0.012 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8033 (pt) cc_final: 0.7554 (pt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1891 time to fit residues: 5.4168 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 39 optimal weight: 0.0670 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 1.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3798 Z= 0.171 Angle : 0.604 7.894 5164 Z= 0.303 Chirality : 0.043 0.140 590 Planarity : 0.006 0.106 668 Dihedral : 5.032 22.171 509 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.74 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.37), residues: 469 helix: -0.63 (0.66), residues: 59 sheet: -1.02 (0.35), residues: 213 loop : -2.90 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.005 0.001 HIS B 135 PHE 0.009 0.001 PHE B 43 TYR 0.014 0.001 TYR B 15 ARG 0.008 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7923 (pt) cc_final: 0.7534 (pt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2283 time to fit residues: 6.7164 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.0970 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 1.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3798 Z= 0.171 Angle : 0.605 7.194 5164 Z= 0.304 Chirality : 0.043 0.154 590 Planarity : 0.007 0.120 668 Dihedral : 4.949 20.131 509 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.74 % Favored : 90.83 % Rotamer: Outliers : 0.24 % Allowed : 1.45 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -2.43 (0.38), residues: 469 helix: -0.46 (0.67), residues: 59 sheet: -0.81 (0.35), residues: 208 loop : -2.84 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 134 HIS 0.003 0.001 HIS B 135 PHE 0.009 0.001 PHE B 43 TYR 0.013 0.001 TYR B 15 ARG 0.013 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 TYR cc_start: 0.6636 (t80) cc_final: 0.6325 (t80) REVERT: B 336 LEU cc_start: 0.8043 (pt) cc_final: 0.7464 (pp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1691 time to fit residues: 5.2836 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 1.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3798 Z= 0.266 Angle : 0.667 6.877 5164 Z= 0.341 Chirality : 0.043 0.143 590 Planarity : 0.007 0.140 668 Dihedral : 5.403 19.765 509 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.45 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.37), residues: 469 helix: -0.63 (0.66), residues: 59 sheet: -0.98 (0.35), residues: 215 loop : -3.02 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 278 HIS 0.009 0.002 HIS B 135 PHE 0.015 0.002 PHE B 335 TYR 0.021 0.002 TYR B 15 ARG 0.015 0.001 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.479 Fit side-chains REVERT: B 336 LEU cc_start: 0.8035 (pt) cc_final: 0.7683 (pp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1884 time to fit residues: 6.0096 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 191 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 = 0.3245 r_free = 0.3245 target = 0.045928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038900 restraints weight = 38471.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039803 restraints weight = 24634.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040449 restraints weight = 17647.910| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 1.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3798 Z= 0.307 Angle : 0.694 6.231 5164 Z= 0.358 Chirality : 0.044 0.205 590 Planarity : 0.006 0.085 668 Dihedral : 5.710 20.456 509 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.30 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -2.96 (0.36), residues: 469 helix: -1.28 (0.64), residues: 59 sheet: -1.19 (0.34), residues: 215 loop : -3.04 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 278 HIS 0.007 0.002 HIS B 135 PHE 0.018 0.002 PHE B 43 TYR 0.016 0.002 TYR B 71 ARG 0.012 0.001 ARG B 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1177.00 seconds wall clock time: 26 minutes 8.10 seconds (1568.10 seconds total)