Starting phenix.real_space_refine on Thu Jul 18 19:41:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2024/7xq0_33387_neut.cif" } resolution = 3.0 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= 0.004 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 4 5.49 5 S 10 5.16 5 C 2189 2.51 5 N 553 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" 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: 3320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3232 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Classifications: {'RNA': 2} Link IDs: {'rna3p': 1} Chain breaks: 1 Time building chain proxies: 3.04, per 1000 atoms: 0.92 Number of scatterers: 3320 At special positions: 0 Unit cell: (78, 75, 67, 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 10 16.00 P 4 15.00 O 564 8.00 N 553 7.00 C 2189 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: 1.66 Conformation dependent library (CDL) restraints added in 583.4 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 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: 21 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.621A pdb=" N TRP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.923A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.879A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.531A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.582A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.414A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.686A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.712A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.540A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 4.142A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.797A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.070A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.586A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.682A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.765A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.962A pdb=" N ILE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 645 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: 0.85 Time building geometry restraints manager: 1.48 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: 973 1.34 - 1.45: 637 1.45 - 1.57: 1781 1.57 - 1.69: 12 1.69 - 1.80: 18 Bond restraints: 3421 Sorted by residual: bond pdb="C1'1 2BA A 601 " pdb="C2'1 2BA A 601 " ideal model delta sigma weight residual 1.532 1.294 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb="C1'1 2BA A 602 " pdb="C2'1 2BA A 602 " ideal model delta sigma weight residual 1.532 1.297 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' 2BA A 601 " pdb=" C2' 2BA A 601 " ideal model delta sigma weight residual 1.541 1.317 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' 2BA A 602 " pdb=" C2' 2BA A 602 " ideal model delta sigma weight residual 1.541 1.318 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb="C1'1 2BA A 601 " pdb="O4'1 2BA A 601 " ideal model delta sigma weight residual 1.408 1.617 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 3416 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.16: 115 107.16 - 114.29: 1981 114.29 - 121.43: 1904 121.43 - 128.57: 642 128.57 - 135.70: 39 Bond angle restraints: 4681 Sorted by residual: angle pdb=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N PRO A 381 " ideal model delta sigma weight residual 120.83 116.29 4.54 6.10e-01 2.69e+00 5.53e+01 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" O1P 2BA A 601 " pdb=" P 2BA A 601 " pdb=" O2P 2BA A 601 " ideal model delta sigma weight residual 121.18 104.63 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1P 2BA A 602 " pdb=" P 2BA A 602 " pdb=" O2P 2BA A 602 " ideal model delta sigma weight residual 121.18 104.64 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb="O1P1 2BA A 602 " pdb=" P1 2BA A 602 " pdb="O2P1 2BA A 602 " ideal model delta sigma weight residual 122.22 106.86 15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 4676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1870 17.70 - 35.39: 137 35.39 - 53.09: 24 53.09 - 70.79: 3 70.79 - 88.48: 3 Dihedral angle restraints: 2037 sinusoidal: 854 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP A 363 " pdb=" C TRP A 363 " pdb=" N LEU A 364 " pdb=" CA LEU A 364 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.099: 514 0.099 - 0.198: 23 0.198 - 0.297: 3 0.297 - 0.396: 0 0.396 - 0.494: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" C2' 2BA A 602 " pdb=" C1' 2BA A 602 " pdb=" C3' 2BA A 602 " pdb=" O2' 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.80 -2.31 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C2' 2BA A 601 " pdb=" C1' 2BA A 601 " pdb=" C3' 2BA A 601 " pdb=" O2' 2BA A 601 " both_signs ideal model delta sigma weight residual False -2.80 -2.34 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb="C2'1 2BA A 602 " pdb="C1'1 2BA A 602 " pdb="C3'1 2BA A 602 " pdb="O2'1 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.67 -2.39 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 539 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 71 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C VAL A 71 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 82 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 70 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.031 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 742 2.77 - 3.30: 3009 3.30 - 3.83: 5785 3.83 - 4.37: 7298 4.37 - 4.90: 11921 Nonbonded interactions: 28755 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.232 2.440 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.258 2.440 nonbonded pdb=" O1P 2BA A 601 " pdb=" N6 2BA A 602 " model vdw 2.328 2.520 nonbonded pdb=" O ARG A 61 " pdb=" OG1 THR A 65 " model vdw 2.336 2.440 nonbonded pdb=" OG SER A 392 " pdb=" OE1 GLU A 394 " model vdw 2.339 2.440 ... (remaining 28750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.780 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.014 0.238 3421 Z= 0.723 Angle : 1.263 16.547 4681 Z= 0.569 Chirality : 0.057 0.494 542 Planarity : 0.006 0.057 552 Dihedral : 13.005 88.484 1277 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.86 % Allowed : 8.36 % Favored : 90.78 % 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: -6.72 (0.21), residues: 398 helix: -4.46 (0.12), residues: 313 sheet: None (None), residues: 0 loop : -3.02 (0.49), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.011 0.001 PHE A 37 TYR 0.009 0.002 TYR A 76 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.364 Fit side-chains REVERT: A 26 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7168 (mmp-170) REVERT: A 62 GLU cc_start: 0.7399 (pp20) cc_final: 0.6862 (tm-30) REVERT: A 122 MET cc_start: 0.8531 (tmm) cc_final: 0.8278 (ttp) REVERT: A 333 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7023 (tpt-90) REVERT: A 416 PHE cc_start: 0.8211 (t80) cc_final: 0.7976 (t80) REVERT: A 451 MET cc_start: 0.6313 (mmt) cc_final: 0.6057 (mmt) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.9378 time to fit residues: 54.6101 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 266 GLN A 277 ASN A 293 ASN A 431 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3421 Z= 0.227 Angle : 0.583 6.334 4681 Z= 0.301 Chirality : 0.039 0.116 542 Planarity : 0.005 0.035 552 Dihedral : 6.128 25.059 574 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 12.39 % Favored : 84.44 % 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: -3.05 (0.33), residues: 398 helix: -1.76 (0.23), residues: 315 sheet: None (None), residues: 0 loop : -2.21 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 114 PHE 0.008 0.001 PHE A 212 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.380 Fit side-chains REVERT: A 26 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6965 (mmp-170) REVERT: A 62 GLU cc_start: 0.7492 (pp20) cc_final: 0.7187 (pm20) REVERT: A 333 ARG cc_start: 0.7599 (tmt170) cc_final: 0.7022 (tpt-90) REVERT: A 416 PHE cc_start: 0.8300 (t80) cc_final: 0.8060 (t80) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.5948 time to fit residues: 31.6023 Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3421 Z= 0.162 Angle : 0.523 7.826 4681 Z= 0.261 Chirality : 0.037 0.114 542 Planarity : 0.003 0.028 552 Dihedral : 5.665 25.685 574 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 14.12 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.40), residues: 398 helix: 0.10 (0.28), residues: 312 sheet: None (None), residues: 0 loop : -2.12 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.012 0.001 PHE A 447 TYR 0.008 0.001 TYR A 92 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.362 Fit side-chains REVERT: A 26 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6874 (mmp-170) REVERT: A 62 GLU cc_start: 0.7499 (pp20) cc_final: 0.7231 (pm20) REVERT: A 333 ARG cc_start: 0.7599 (tmt170) cc_final: 0.7026 (tpt-90) REVERT: A 416 PHE cc_start: 0.8250 (t80) cc_final: 0.8033 (t80) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.6641 time to fit residues: 34.6076 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3421 Z= 0.217 Angle : 0.526 7.085 4681 Z= 0.264 Chirality : 0.040 0.161 542 Planarity : 0.003 0.028 552 Dihedral : 5.697 24.377 574 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.75 % Allowed : 14.12 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.42), residues: 398 helix: 0.71 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.91 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.018 0.001 PHE A 447 TYR 0.010 0.001 TYR A 438 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.363 Fit side-chains REVERT: A 26 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6868 (mmp-170) REVERT: A 62 GLU cc_start: 0.7493 (pp20) cc_final: 0.7207 (pm20) REVERT: A 333 ARG cc_start: 0.7602 (tmt170) cc_final: 0.7020 (tpt-90) REVERT: A 416 PHE cc_start: 0.8357 (t80) cc_final: 0.8090 (t80) REVERT: A 451 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7073 (mmt) outliers start: 13 outliers final: 5 residues processed: 47 average time/residue: 0.6690 time to fit residues: 33.3230 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 451 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3421 Z= 0.212 Angle : 0.514 7.780 4681 Z= 0.258 Chirality : 0.039 0.129 542 Planarity : 0.003 0.029 552 Dihedral : 5.657 24.801 574 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.03 % Allowed : 14.99 % Favored : 80.98 % 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: 0.60 (0.42), residues: 398 helix: 0.99 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.80 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.018 0.001 PHE A 447 TYR 0.010 0.001 TYR A 438 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.374 Fit side-chains REVERT: A 26 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6892 (mmp-170) REVERT: A 62 GLU cc_start: 0.7461 (pp20) cc_final: 0.7041 (pm20) REVERT: A 333 ARG cc_start: 0.7589 (tmt170) cc_final: 0.7020 (tpt-90) REVERT: A 416 PHE cc_start: 0.8312 (t80) cc_final: 0.8070 (t80) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.6923 time to fit residues: 33.7371 Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3421 Z= 0.221 Angle : 0.528 7.787 4681 Z= 0.260 Chirality : 0.039 0.119 542 Planarity : 0.003 0.030 552 Dihedral : 5.671 25.495 574 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 15.85 % Favored : 80.98 % 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: 0.82 (0.42), residues: 398 helix: 1.15 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.74 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.018 0.001 PHE A 84 TYR 0.010 0.001 TYR A 438 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.376 Fit side-chains REVERT: A 26 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6849 (mmp-170) REVERT: A 62 GLU cc_start: 0.7453 (pp20) cc_final: 0.6838 (pm20) REVERT: A 333 ARG cc_start: 0.7586 (tmt170) cc_final: 0.7016 (tpt-90) REVERT: A 416 PHE cc_start: 0.8298 (t80) cc_final: 0.8084 (t80) REVERT: A 451 MET cc_start: 0.6887 (mmt) cc_final: 0.6645 (mmt) REVERT: A 452 LEU cc_start: 0.8149 (tm) cc_final: 0.7942 (tt) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.7604 time to fit residues: 37.5610 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3421 Z= 0.185 Angle : 0.507 7.566 4681 Z= 0.252 Chirality : 0.038 0.133 542 Planarity : 0.003 0.030 552 Dihedral : 5.565 25.812 574 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.17 % Allowed : 17.29 % Favored : 79.54 % 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: 1.08 (0.42), residues: 398 helix: 1.35 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.74 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.010 0.001 PHE A 447 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.328 Fit side-chains REVERT: A 26 ARG cc_start: 0.7300 (mtp85) cc_final: 0.6840 (mmp-170) REVERT: A 62 GLU cc_start: 0.7454 (pp20) cc_final: 0.6835 (pm20) REVERT: A 333 ARG cc_start: 0.7518 (tmt170) cc_final: 0.6969 (tpt-90) REVERT: A 452 LEU cc_start: 0.8117 (tm) cc_final: 0.7904 (tt) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.7257 time to fit residues: 33.8463 Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3421 Z= 0.187 Angle : 0.506 7.279 4681 Z= 0.252 Chirality : 0.038 0.144 542 Planarity : 0.003 0.030 552 Dihedral : 5.539 26.160 574 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.17 % Allowed : 17.58 % Favored : 79.25 % 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: 1.31 (0.42), residues: 398 helix: 1.53 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.73 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.022 0.001 PHE A 84 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.349 Fit side-chains REVERT: A 26 ARG cc_start: 0.7289 (mtp85) cc_final: 0.6831 (mmp-170) REVERT: A 62 GLU cc_start: 0.7467 (pp20) cc_final: 0.6817 (pm20) REVERT: A 289 HIS cc_start: 0.8657 (m-70) cc_final: 0.8283 (m170) REVERT: A 333 ARG cc_start: 0.7515 (tmt170) cc_final: 0.6972 (tpt-90) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.6833 time to fit residues: 33.9336 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3421 Z= 0.187 Angle : 0.529 8.949 4681 Z= 0.259 Chirality : 0.039 0.192 542 Planarity : 0.003 0.030 552 Dihedral : 5.524 26.441 574 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.31 % Allowed : 18.73 % Favored : 78.96 % 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: 1.38 (0.42), residues: 398 helix: 1.58 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.70 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.023 0.001 PHE A 84 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.362 Fit side-chains REVERT: A 26 ARG cc_start: 0.7289 (mtp85) cc_final: 0.6835 (mmp-170) REVERT: A 62 GLU cc_start: 0.7442 (pp20) cc_final: 0.6807 (pm20) REVERT: A 289 HIS cc_start: 0.8689 (m-70) cc_final: 0.8321 (m170) REVERT: A 333 ARG cc_start: 0.7522 (tmt170) cc_final: 0.6975 (tpt-90) REVERT: A 451 MET cc_start: 0.7184 (mpp) cc_final: 0.6945 (mmt) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.8490 time to fit residues: 39.1520 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3421 Z= 0.227 Angle : 0.541 7.195 4681 Z= 0.267 Chirality : 0.040 0.189 542 Planarity : 0.003 0.031 552 Dihedral : 5.632 27.056 574 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 19.02 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.42), residues: 398 helix: 1.58 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.024 0.001 PHE A 447 TYR 0.010 0.001 TYR A 438 ARG 0.001 0.000 ARG A 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.381 Fit side-chains REVERT: A 26 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6845 (mmp-170) REVERT: A 62 GLU cc_start: 0.7493 (pp20) cc_final: 0.6820 (pm20) REVERT: A 333 ARG cc_start: 0.7563 (tmt170) cc_final: 0.7013 (tpt-90) REVERT: A 451 MET cc_start: 0.7197 (mpp) cc_final: 0.6974 (mmt) REVERT: A 452 LEU cc_start: 0.8075 (tm) cc_final: 0.7875 (tt) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.8438 time to fit residues: 36.2865 Evaluate side-chains 40 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 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 = 0.3252 r_free = 0.3252 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095379 restraints weight = 3727.578| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.77 r_work: 0.2910 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3421 Z= 0.211 Angle : 0.531 7.308 4681 Z= 0.262 Chirality : 0.040 0.188 542 Planarity : 0.003 0.031 552 Dihedral : 5.605 27.163 574 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.59 % Allowed : 18.73 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.42), residues: 398 helix: 1.64 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.026 0.001 PHE A 84 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.69 seconds wall clock time: 28 minutes 1.69 seconds (1681.69 seconds total)