Starting phenix.real_space_refine on Sun Mar 10 18:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/03_2024/5ly6_4118.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/03_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_4118/03_2024/5ly6_4118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/03_2024/5ly6_4118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/03_2024/5ly6_4118.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/03_2024/5ly6_4118.pdb" } 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 Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B ARG 437": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 2.54, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 823.3 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: 0.47 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: 0.95 Time building geometry restraints manager: 1.45 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: 97.79 - 105.86: 78 105.86 - 113.94: 2224 113.94 - 122.01: 2178 122.01 - 130.09: 659 130.09 - 138.16: 25 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 2.520 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 2.520 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 9.280 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- 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 : 0.459 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: 0.2024 time to fit residues: 45.0166 Evaluate side-chains 87 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 47 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 6.0126 ------------------------------------------------------------------------------- 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 ** 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 197 GLN B 245 GLN B 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 3798 Z= 0.386 Angle : 0.873 8.824 5164 Z= 0.455 Chirality : 0.049 0.246 590 Planarity : 0.009 0.106 668 Dihedral : 5.571 26.026 509 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.85 % Allowed : 12.79 % Favored : 86.35 % 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: -4.22 (0.35), residues: 469 helix: -0.90 (0.65), residues: 61 sheet: -1.98 (0.37), residues: 189 loop : -4.21 (0.32), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 134 HIS 0.008 0.002 HIS B 135 PHE 0.025 0.003 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 39 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.5892 (pmm) cc_final: 0.4397 (ppp) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1985 time to fit residues: 9.5500 Evaluate side-chains 25 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 85 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.8552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 3798 Z= 0.322 Angle : 0.734 7.541 5164 Z= 0.382 Chirality : 0.045 0.226 590 Planarity : 0.008 0.091 668 Dihedral : 5.208 30.968 509 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.94 % Favored : 87.42 % Rotamer: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.85 (0.36), residues: 469 helix: -0.79 (0.62), residues: 67 sheet: -1.93 (0.34), residues: 222 loop : -3.98 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.011 0.002 HIS B 135 PHE 0.011 0.002 PHE B 335 TYR 0.014 0.002 TYR B 15 ARG 0.009 0.001 ARG B 69 *********************** 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 29 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8111 (pt) cc_final: 0.7303 (pp) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.2121 time to fit residues: 7.7126 Evaluate side-chains 24 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.9353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3798 Z= 0.285 Angle : 0.718 16.412 5164 Z= 0.356 Chirality : 0.044 0.269 590 Planarity : 0.006 0.082 668 Dihedral : 5.065 28.076 509 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.74 % Favored : 90.83 % Rotamer: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % 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: -3.34 (0.36), residues: 469 helix: -0.95 (0.58), residues: 74 sheet: -1.45 (0.34), residues: 224 loop : -3.76 (0.37), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 278 HIS 0.008 0.001 HIS B 135 PHE 0.009 0.002 PHE B 180 TYR 0.017 0.002 TYR B 15 ARG 0.004 0.001 ARG B 69 *********************** 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 29 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8139 (pt) cc_final: 0.7643 (pt) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.2019 time to fit residues: 7.4719 Evaluate side-chains 21 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.9943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3798 Z= 0.263 Angle : 0.668 10.060 5164 Z= 0.342 Chirality : 0.043 0.179 590 Planarity : 0.005 0.076 668 Dihedral : 5.007 21.772 509 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.02 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.83 (0.37), residues: 469 helix: -0.39 (0.64), residues: 67 sheet: -1.26 (0.32), residues: 231 loop : -3.25 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 433 HIS 0.011 0.002 HIS B 135 PHE 0.009 0.002 PHE B 43 TYR 0.017 0.002 TYR B 371 ARG 0.004 0.001 ARG B 69 *********************** 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 26 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8200 (pt) cc_final: 0.7590 (pt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.2476 time to fit residues: 8.0093 Evaluate side-chains 21 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 0.0470 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.6102 ------------------------------------------------------------------------------- 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: 0.6799 moved from start: 1.0168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3798 Z= 0.192 Angle : 0.627 9.042 5164 Z= 0.311 Chirality : 0.043 0.152 590 Planarity : 0.005 0.069 668 Dihedral : 4.934 25.022 509 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.32 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -2.51 (0.37), residues: 469 helix: -0.22 (0.64), residues: 67 sheet: -0.95 (0.34), residues: 218 loop : -3.08 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 134 HIS 0.008 0.001 HIS B 135 PHE 0.010 0.001 PHE B 43 TYR 0.013 0.001 TYR B 15 ARG 0.002 0.000 ARG B 94 *********************** 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 : 0.452 Fit side-chains revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8075 (pt) cc_final: 0.7547 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1718 time to fit residues: 5.8031 Evaluate side-chains 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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 85 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: 0.6894 moved from start: 1.0528 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= 0.246 Angle : 0.634 7.398 5164 Z= 0.320 Chirality : 0.041 0.143 590 Planarity : 0.005 0.064 668 Dihedral : 5.040 19.232 509 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.23 % Favored : 89.34 % 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: -2.50 (0.38), residues: 469 helix: -0.25 (0.69), residues: 60 sheet: -0.91 (0.34), residues: 218 loop : -3.01 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 134 HIS 0.007 0.001 HIS B 135 PHE 0.013 0.002 PHE B 43 TYR 0.015 0.002 TYR B 15 ARG 0.004 0.001 ARG B 69 *********************** 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 23 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: B 336 LEU cc_start: 0.8054 (pt) cc_final: 0.7058 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1797 time to fit residues: 5.4820 Evaluate side-chains 18 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 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 : 0.006 0.065 3798 Z= 0.433 Angle : 0.808 10.789 5164 Z= 0.415 Chirality : 0.044 0.153 590 Planarity : 0.006 0.062 668 Dihedral : 5.976 20.589 509 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.15 % Favored : 87.42 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -3.09 (0.36), residues: 469 helix: -1.06 (0.65), residues: 59 sheet: -1.35 (0.33), residues: 203 loop : -3.06 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 134 HIS 0.012 0.002 HIS B 135 PHE 0.020 0.003 PHE B 43 TYR 0.023 0.003 TYR B 15 ARG 0.008 0.001 ARG B 69 *********************** 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 : 0.451 Fit side-chains REVERT: B 336 LEU cc_start: 0.8134 (pt) cc_final: 0.7292 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1457 time to fit residues: 4.7313 Evaluate side-chains 15 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 28 optimal weight: 8.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** 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: 0.6977 moved from start: 1.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3798 Z= 0.290 Angle : 0.670 6.480 5164 Z= 0.343 Chirality : 0.043 0.146 590 Planarity : 0.005 0.062 668 Dihedral : 5.537 18.828 509 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.87 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % 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: -3.07 (0.36), residues: 469 helix: -0.89 (0.70), residues: 53 sheet: -1.43 (0.32), residues: 212 loop : -2.97 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 134 HIS 0.009 0.002 HIS B 135 PHE 0.016 0.002 PHE B 43 TYR 0.017 0.002 TYR B 15 ARG 0.006 0.001 ARG B 69 *********************** 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 21 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.417 Fit side-chains REVERT: B 336 LEU cc_start: 0.8017 (pt) cc_final: 0.7118 (pp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1479 time to fit residues: 4.4330 Evaluate side-chains 15 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 9.9990 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** 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: 0.6951 moved from start: 1.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3798 Z= 0.259 Angle : 0.650 7.216 5164 Z= 0.331 Chirality : 0.042 0.141 590 Planarity : 0.004 0.058 668 Dihedral : 5.426 18.880 509 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.45 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -3.00 (0.36), residues: 469 helix: -0.83 (0.69), residues: 53 sheet: -1.42 (0.32), residues: 214 loop : -2.91 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.008 0.001 HIS B 135 PHE 0.014 0.002 PHE B 43 TYR 0.017 0.002 TYR B 15 ARG 0.004 0.001 ARG B 69 ********************** 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 23 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.478 Fit side-chains REVERT: B 336 LEU cc_start: 0.7989 (pt) cc_final: 0.7105 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1867 time to fit residues: 5.7394 Evaluate side-chains 16 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3261 r_free = 0.3261 target = 0.046151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.038945 restraints weight = 38043.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.039824 restraints weight = 24958.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040456 restraints weight = 18216.689| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 1.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 3798 Z= 0.219 Angle : 0.611 6.102 5164 Z= 0.310 Chirality : 0.042 0.169 590 Planarity : 0.004 0.056 668 Dihedral : 5.169 17.416 509 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.23 % Favored : 89.34 % 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: -2.86 (0.36), residues: 469 helix: -0.75 (0.69), residues: 53 sheet: -1.33 (0.33), residues: 212 loop : -2.79 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 134 HIS 0.006 0.001 HIS B 135 PHE 0.012 0.001 PHE B 43 TYR 0.015 0.002 TYR B 15 ARG 0.004 0.001 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.14 seconds wall clock time: 21 minutes 46.51 seconds (1306.51 seconds total)