Starting phenix.real_space_refine on Thu Jul 18 19:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znb_60266/07_2024/8znb_60266.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2113 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} bond proxies already assigned to first conformer: 3321 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 69 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 21} Link IDs: {None: 21} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 89 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 89 " occ=0.50 Time building chain proxies: 4.20, per 1000 atoms: 1.26 Number of scatterers: 3342 At special positions: 0 Unit cell: (66.176, 61.664, 73.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 648 8.00 N 564 7.00 C 2113 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 1.1 seconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 56.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.745A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.795A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.722A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.565A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.701A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.008A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.676A pdb=" N ALA A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.548A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.985A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.291A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 547 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: 0.98 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 938 1.33 - 1.45: 548 1.45 - 1.57: 1881 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3399 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.603 0.154 3.50e-02 8.16e+02 1.93e+01 bond pdb=" C PRO A 252 " pdb=" N ASP A 253 " ideal model delta sigma weight residual 1.335 1.384 -0.050 1.36e-02 5.41e+03 1.33e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.90e-02 1.19e+03 1.02e+01 bond pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 1.368 1.448 -0.080 3.20e-02 9.77e+02 6.22e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.52: 162 107.52 - 114.30: 1937 114.30 - 121.09: 1550 121.09 - 127.87: 931 127.87 - 134.66: 37 Bond angle restraints: 4617 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 132.14 -24.40 1.95e+00 2.62e-01 1.56e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 118.94 -15.10 1.91e+00 2.73e-01 6.22e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 119.33 -14.40 2.66e+00 1.41e-01 2.93e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.57 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.31 5.15 1.17e+00 7.36e-01 1.95e+01 ... (remaining 4612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1819 17.98 - 35.97: 143 35.97 - 53.95: 36 53.95 - 71.94: 10 71.94 - 89.92: 7 Dihedral angle restraints: 2015 sinusoidal: 822 harmonic: 1193 Sorted by residual: dihedral pdb=" CA THR A 148 " pdb=" C THR A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 400 0.052 - 0.104: 84 0.104 - 0.156: 16 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.41 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 499 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 150 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 393 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE A 393 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 393 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A 394 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 394 " -0.013 2.00e-02 2.50e+03 1.09e-02 1.79e+00 pdb=" CG HIS A 394 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 394 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 394 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 394 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 394 " -0.011 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1290 2.92 - 3.41: 3444 3.41 - 3.91: 5994 3.91 - 4.40: 6792 4.40 - 4.90: 10962 Nonbonded interactions: 28482 Sorted by model distance: nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.421 2.520 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.443 2.440 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.449 2.440 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.449 2.520 nonbonded pdb=" NZ LYS A 177 " pdb=" OE2 GLU A 354 " model vdw 2.464 2.520 ... (remaining 28477 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 16.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.007 0.221 3399 Z= 0.492 Angle : 0.945 24.400 4617 Z= 0.541 Chirality : 0.047 0.260 502 Planarity : 0.005 0.045 589 Dihedral : 15.547 89.920 1255 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 0.59 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.41), residues: 417 helix: 1.83 (0.37), residues: 202 sheet: -0.52 (0.69), residues: 64 loop : -1.15 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 92 HIS 0.008 0.002 HIS A 394 PHE 0.010 0.002 PHE A 341 TYR 0.013 0.002 TYR A 226 ARG 0.003 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.424 Fit side-chains REVERT: A 187 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: A 333 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8192 (mtpt) REVERT: A 386 ASN cc_start: 0.8503 (m-40) cc_final: 0.8166 (m110) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7957 (t70) outliers start: 7 outliers final: 0 residues processed: 86 average time/residue: 1.2259 time to fit residues: 108.3624 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 267 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3399 Z= 0.235 Angle : 0.535 8.654 4617 Z= 0.282 Chirality : 0.046 0.142 502 Planarity : 0.005 0.047 589 Dihedral : 6.415 53.306 470 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.24 % Allowed : 11.47 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.41), residues: 417 helix: 2.05 (0.37), residues: 202 sheet: -0.09 (0.71), residues: 62 loop : -1.00 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.382 Fit side-chains REVERT: A 187 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7626 (ttm110) REVERT: A 214 LYS cc_start: 0.8481 (mttm) cc_final: 0.8159 (mppt) REVERT: A 333 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8249 (mtpt) REVERT: A 388 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.7797 (t70) outliers start: 11 outliers final: 2 residues processed: 68 average time/residue: 1.3236 time to fit residues: 92.4181 Evaluate side-chains 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0010 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3399 Z= 0.193 Angle : 0.493 5.429 4617 Z= 0.265 Chirality : 0.045 0.152 502 Planarity : 0.004 0.048 589 Dihedral : 6.287 52.440 470 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 14.41 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.42), residues: 417 helix: 2.08 (0.37), residues: 206 sheet: -0.60 (0.68), residues: 69 loop : -0.99 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.342 Fit side-chains REVERT: A 187 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7504 (ttm110) REVERT: A 214 LYS cc_start: 0.8631 (mttm) cc_final: 0.8331 (mttp) REVERT: A 252 PRO cc_start: 0.8056 (Cg_endo) cc_final: 0.7797 (Cg_exo) REVERT: A 255 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 297 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8468 (pp) REVERT: A 333 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8242 (mtpt) REVERT: A 388 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.7899 (t70) outliers start: 9 outliers final: 1 residues processed: 61 average time/residue: 1.3048 time to fit residues: 81.7160 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3399 Z= 0.141 Angle : 0.455 5.169 4617 Z= 0.243 Chirality : 0.043 0.142 502 Planarity : 0.004 0.047 589 Dihedral : 6.045 55.236 470 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.88 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.42), residues: 417 helix: 2.11 (0.37), residues: 209 sheet: -0.20 (0.72), residues: 64 loop : -0.99 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.006 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.344 Fit side-chains REVERT: A 297 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 333 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8250 (mtmt) REVERT: A 388 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.7853 (t70) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.2083 time to fit residues: 74.6139 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3399 Z= 0.136 Angle : 0.477 9.787 4617 Z= 0.242 Chirality : 0.042 0.150 502 Planarity : 0.004 0.051 589 Dihedral : 5.197 57.829 466 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.43), residues: 417 helix: 2.17 (0.37), residues: 209 sheet: -0.01 (0.74), residues: 62 loop : -0.82 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.293 Fit side-chains REVERT: A 214 LYS cc_start: 0.8902 (mttm) cc_final: 0.8446 (mttt) REVERT: A 297 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 328 ASP cc_start: 0.7681 (m-30) cc_final: 0.7481 (m-30) REVERT: A 333 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8199 (mtmt) REVERT: A 388 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7824 (t70) REVERT: A 389 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8368 (mmmm) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 1.2504 time to fit residues: 77.1704 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.0170 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 234 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3399 Z= 0.191 Angle : 0.490 9.410 4617 Z= 0.254 Chirality : 0.044 0.157 502 Planarity : 0.005 0.046 589 Dihedral : 5.434 59.135 466 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.47 % Allowed : 17.06 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 417 helix: 2.17 (0.37), residues: 207 sheet: -0.09 (0.73), residues: 62 loop : -0.98 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.411 Fit side-chains REVERT: A 214 LYS cc_start: 0.8915 (mttm) cc_final: 0.8421 (mttp) REVERT: A 297 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8426 (pp) REVERT: A 333 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8132 (mtpt) REVERT: A 388 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.7806 (t70) REVERT: A 389 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8406 (mmmm) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 1.3169 time to fit residues: 73.3082 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3399 Z= 0.210 Angle : 0.515 11.475 4617 Z= 0.265 Chirality : 0.045 0.163 502 Planarity : 0.004 0.043 589 Dihedral : 5.547 59.733 466 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 17.94 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.42), residues: 417 helix: 2.09 (0.37), residues: 207 sheet: -0.17 (0.72), residues: 63 loop : -1.01 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.010 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.379 Fit side-chains REVERT: A 214 LYS cc_start: 0.8862 (mttm) cc_final: 0.8399 (mttt) REVERT: A 297 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 333 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8224 (mtpt) REVERT: A 388 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.7786 (t70) REVERT: A 389 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8403 (mmmm) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 1.2382 time to fit residues: 71.4356 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3399 Z= 0.156 Angle : 0.482 9.751 4617 Z= 0.248 Chirality : 0.043 0.157 502 Planarity : 0.004 0.044 589 Dihedral : 5.302 59.126 466 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 18.24 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 417 helix: 2.12 (0.37), residues: 209 sheet: -0.18 (0.72), residues: 63 loop : -0.89 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.346 Fit side-chains REVERT: A 214 LYS cc_start: 0.8836 (mttm) cc_final: 0.8349 (mttt) REVERT: A 297 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8389 (pp) REVERT: A 333 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8116 (mtpt) REVERT: A 388 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.7669 (t70) REVERT: A 389 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8335 (mmmm) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 1.1993 time to fit residues: 67.9958 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3399 Z= 0.159 Angle : 0.488 9.946 4617 Z= 0.250 Chirality : 0.043 0.161 502 Planarity : 0.004 0.043 589 Dihedral : 5.263 58.590 466 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 17.94 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.42), residues: 417 helix: 2.14 (0.37), residues: 209 sheet: -0.08 (0.72), residues: 62 loop : -0.90 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.366 Fit side-chains REVERT: A 214 LYS cc_start: 0.8811 (mttm) cc_final: 0.8332 (mttt) REVERT: A 297 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 333 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8098 (mtpt) REVERT: A 388 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.7620 (t70) outliers start: 4 outliers final: 1 residues processed: 56 average time/residue: 1.2899 time to fit residues: 74.4299 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3399 Z= 0.149 Angle : 0.496 9.180 4617 Z= 0.248 Chirality : 0.043 0.163 502 Planarity : 0.004 0.043 589 Dihedral : 5.139 58.020 466 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 18.24 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 417 helix: 2.18 (0.37), residues: 209 sheet: -0.06 (0.73), residues: 62 loop : -0.86 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.391 Fit side-chains REVERT: A 214 LYS cc_start: 0.8833 (mttm) cc_final: 0.8385 (mttt) REVERT: A 297 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8342 (pp) REVERT: A 333 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8107 (mtpt) REVERT: A 388 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.7672 (t70) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 1.2152 time to fit residues: 71.4717 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 193 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 = 0.3541 r_free = 0.3541 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090756 restraints weight = 11584.937| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.91 r_work: 0.2761 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3399 Z= 0.173 Angle : 0.506 9.476 4617 Z= 0.255 Chirality : 0.043 0.165 502 Planarity : 0.004 0.043 589 Dihedral : 5.238 58.190 466 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.88 % Allowed : 17.94 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.42), residues: 417 helix: 2.16 (0.37), residues: 209 sheet: -0.18 (0.73), residues: 63 loop : -0.84 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.39 seconds wall clock time: 35 minutes 50.28 seconds (2150.28 seconds total)