Starting phenix.real_space_refine (version: dev) on Fri Feb 17 06:59:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/02_2023/5ly6_4118.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/02_2023/5ly6_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_4118/02_2023/5ly6_4118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/02_2023/5ly6_4118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/02_2023/5ly6_4118.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ly6_4118/02_2023/5ly6_4118.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 2.76, per 1000 atoms: 0.74 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: 1.49 Conformation dependent library (CDL) restraints added in 708.7 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: 0.23 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: 1.00 Time building geometry restraints manager: 1.62 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 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. 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: 3.000 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: 10.130 Check model and map are aligned: 0.060 Process input model: 15.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 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 % 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 *********************** 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 : 0.434 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 outliers start: 150 outliers final: 33 residues processed: 192 average time/residue: 0.2123 time to fit residues: 47.2414 Evaluate side-chains 79 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 46 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1026 time to fit residues: 4.9700 ------------------------------------------------------------------------------- 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: 0.0470 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 85 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 3798 Z= 0.267 Angle : 0.797 8.890 5164 Z= 0.410 Chirality : 0.048 0.218 590 Planarity : 0.009 0.107 668 Dihedral : 5.123 26.558 509 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.09 % Favored : 88.06 % Rotamer Outliers : 0.97 % 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: -4.05 (0.36), residues: 469 helix: -0.14 (0.71), residues: 61 sheet: -2.01 (0.36), residues: 187 loop : -4.15 (0.33), residues: 221 *********************** 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 48 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.2023 time to fit residues: 11.8751 Evaluate side-chains 25 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0385 time to fit residues: 0.7748 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- 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 ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS B 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.7995 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= 0.240 Angle : 0.668 7.662 5164 Z= 0.342 Chirality : 0.044 0.199 590 Planarity : 0.007 0.092 668 Dihedral : 4.570 29.191 509 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 10.23 % Favored : 88.91 % Rotamer Outliers : 0.24 % 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: 0.09 (0.67), residues: 66 sheet: -1.47 (0.39), residues: 179 loop : -3.83 (0.33), residues: 224 *********************** 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 35 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1793 time to fit residues: 8.1347 Evaluate side-chains 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5811 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 156 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.9779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 3798 Z= 0.445 Angle : 0.908 12.841 5164 Z= 0.463 Chirality : 0.049 0.296 590 Planarity : 0.007 0.080 668 Dihedral : 5.771 27.884 509 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.09 % Favored : 88.49 % Rotamer Outliers : 0.24 % 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: -3.72 (0.35), residues: 469 helix: -1.69 (0.51), residues: 66 sheet: -1.65 (0.33), residues: 221 loop : -3.73 (0.38), residues: 182 *********************** 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 : 0.427 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2445 time to fit residues: 8.8361 Evaluate side-chains 17 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7848 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 1.0023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 3798 Z= 0.242 Angle : 0.675 9.451 5164 Z= 0.342 Chirality : 0.043 0.185 590 Planarity : 0.005 0.076 668 Dihedral : 4.942 22.145 509 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.96 % Favored : 90.62 % Rotamer Outliers : 0.00 % 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: -3.28 (0.35), residues: 469 helix: -1.44 (0.54), residues: 72 sheet: -1.14 (0.34), residues: 213 loop : -3.74 (0.36), residues: 184 *********************** 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 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.472 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1693 time to fit residues: 4.8092 Evaluate side-chains 13 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6518 ------------------------------------------------------------------------------- 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: 0.0980 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6549 moved from start: 1.0255 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= 0.193 Angle : 0.588 7.374 5164 Z= 0.297 Chirality : 0.042 0.142 590 Planarity : 0.005 0.070 668 Dihedral : 4.618 21.050 509 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.10 % Favored : 91.47 % Rotamer Outliers : 0.00 % 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: -2.88 (0.36), residues: 469 helix: -0.91 (0.57), residues: 71 sheet: -0.92 (0.34), residues: 205 loop : -3.44 (0.38), residues: 193 *********************** 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 21 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1555 time to fit residues: 4.5592 Evaluate side-chains 14 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5860 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 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: 0.6637 moved from start: 1.0517 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= 0.239 Angle : 0.617 7.115 5164 Z= 0.313 Chirality : 0.041 0.146 590 Planarity : 0.005 0.064 668 Dihedral : 4.835 17.651 509 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.81 % Favored : 89.77 % Rotamer Outliers : 0.00 % 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: -2.71 (0.36), residues: 469 helix: -0.86 (0.60), residues: 65 sheet: -0.88 (0.34), residues: 205 loop : -3.14 (0.39), residues: 199 *********************** 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 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.473 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1679 time to fit residues: 4.7269 Evaluate side-chains 14 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6586 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** 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: 0.6740 moved from start: 1.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 3798 Z= 0.307 Angle : 0.685 6.342 5164 Z= 0.353 Chirality : 0.042 0.147 590 Planarity : 0.005 0.061 668 Dihedral : 5.283 18.447 509 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.45 % Favored : 89.13 % Rotamer Outliers : 0.00 % 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: -2.76 (0.36), residues: 469 helix: -1.15 (0.59), residues: 65 sheet: -0.92 (0.33), residues: 219 loop : -3.18 (0.41), residues: 185 *********************** 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 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.456 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1629 time to fit residues: 4.7156 Evaluate side-chains 14 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6449 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 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: 0.6715 moved from start: 1.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 3798 Z= 0.263 Angle : 0.630 6.075 5164 Z= 0.322 Chirality : 0.042 0.168 590 Planarity : 0.004 0.060 668 Dihedral : 5.090 18.759 509 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.81 % Favored : 89.77 % Rotamer Outliers : 0.00 % 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: -2.71 (0.36), residues: 469 helix: -1.08 (0.60), residues: 65 sheet: -0.92 (0.33), residues: 219 loop : -3.12 (0.41), residues: 185 *********************** 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 20 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1600 time to fit residues: 4.5680 Evaluate side-chains 13 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6344 ------------------------------------------------------------------------------- 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: 40.0000 chunk 29 optimal weight: 0.0670 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** 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: 0.6654 moved from start: 1.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 3798 Z= 0.208 Angle : 0.593 6.072 5164 Z= 0.299 Chirality : 0.041 0.154 590 Planarity : 0.004 0.058 668 Dihedral : 4.933 20.583 509 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.96 % Favored : 90.62 % Rotamer Outliers : 0.24 % 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: -2.49 (0.37), residues: 469 helix: -0.77 (0.63), residues: 65 sheet: -0.80 (0.34), residues: 214 loop : -2.97 (0.41), residues: 190 ********************** 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 22 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.486 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1587 time to fit residues: 4.9472 Evaluate side-chains 13 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6225 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.047273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.040105 restraints weight = 38951.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041052 restraints weight = 24129.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041721 restraints weight = 17065.070| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 1.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 3798 Z= 0.246 Angle : 0.617 5.975 5164 Z= 0.314 Chirality : 0.041 0.144 590 Planarity : 0.004 0.055 668 Dihedral : 5.067 20.722 509 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.66 % Favored : 88.91 % Rotamer Outliers : 0.00 % 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: -2.62 (0.37), residues: 469 helix: -0.77 (0.62), residues: 65 sheet: -1.01 (0.34), residues: 223 loop : -2.98 (0.43), residues: 181 =============================================================================== Job complete usr+sys time: 1142.92 seconds wall clock time: 21 minutes 35.21 seconds (1295.21 seconds total)