Starting phenix.real_space_refine on Mon Sep 23 19:29:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/09_2024/8vzo_43684.cif" } resolution = 2.49 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= 0.032 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3152 2.51 5 N 765 2.21 5 O 853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3235 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 15, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 541 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.56, per 1000 atoms: 0.74 Number of scatterers: 4796 At special positions: 0 Unit cell: (74.7, 64.74, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 853 8.00 N 765 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 552.7 milliseconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 5 sheets defined 62.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.952A pdb=" N VAL A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.522A pdb=" N ASN A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.815A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.982A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.541A pdb=" N ILE A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.582A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.516A pdb=" N CYS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.674A pdb=" N ALA A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.617A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 removed outlier: 4.553A pdb=" N ASN A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 395 removed outlier: 3.716A pdb=" N LYS A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 423 through 453 removed outlier: 4.184A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 488 removed outlier: 3.639A pdb=" N ASN A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 removed outlier: 3.530A pdb=" N GLY A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.719A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.968A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU B 21 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.225A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 121 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.225A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 68 329 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 727 1.30 - 1.43: 1430 1.43 - 1.55: 2723 1.55 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4924 Sorted by residual: bond pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" CA SER A 194 " pdb=" CB SER A 194 " ideal model delta sigma weight residual 1.535 1.457 0.077 1.51e-02 4.39e+03 2.63e+01 bond pdb=" C HIS A 198 " pdb=" O HIS A 198 " ideal model delta sigma weight residual 1.236 1.170 0.065 1.28e-02 6.10e+03 2.61e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.528 1.461 0.066 1.35e-02 5.49e+03 2.41e+01 bond pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.473 1.404 0.069 1.40e-02 5.10e+03 2.41e+01 ... (remaining 4919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5474 2.26 - 4.52: 1021 4.52 - 6.78: 162 6.78 - 9.04: 38 9.04 - 11.30: 5 Bond angle restraints: 6700 Sorted by residual: angle pdb=" N ASP B 93 " pdb=" CA ASP B 93 " pdb=" C ASP B 93 " ideal model delta sigma weight residual 112.88 102.80 10.08 1.29e+00 6.01e-01 6.11e+01 angle pdb=" N LYS A 329 " pdb=" CA LYS A 329 " pdb=" C LYS A 329 " ideal model delta sigma weight residual 113.17 103.46 9.71 1.26e+00 6.30e-01 5.93e+01 angle pdb=" CA PHE D 99 " pdb=" CB PHE D 99 " pdb=" CG PHE D 99 " ideal model delta sigma weight residual 113.80 121.01 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" N GLY B 18 " pdb=" CA GLY B 18 " pdb=" C GLY B 18 " ideal model delta sigma weight residual 115.36 106.09 9.27 1.33e+00 5.65e-01 4.85e+01 angle pdb=" CA TYR A 397 " pdb=" C TYR A 397 " pdb=" N LYS A 398 " ideal model delta sigma weight residual 117.48 126.79 -9.31 1.41e+00 5.03e-01 4.36e+01 ... (remaining 6695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2544 17.52 - 35.03: 205 35.03 - 52.55: 56 52.55 - 70.07: 13 70.07 - 87.58: 7 Dihedral angle restraints: 2825 sinusoidal: 1053 harmonic: 1772 Sorted by residual: dihedral pdb=" CD ARG A 174 " pdb=" NE ARG A 174 " pdb=" CZ ARG A 174 " pdb=" NH1 ARG A 174 " ideal model delta sinusoidal sigma weight residual 0.00 -68.40 68.40 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " pdb=" CZ ARG B 90 " pdb=" NH1 ARG B 90 " ideal model delta sinusoidal sigma weight residual 0.00 57.15 -57.15 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CD ARG A 515 " pdb=" NE ARG A 515 " pdb=" CZ ARG A 515 " pdb=" NH1 ARG A 515 " ideal model delta sinusoidal sigma weight residual 0.00 44.54 -44.54 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 2822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 511 0.089 - 0.178: 187 0.178 - 0.267: 48 0.267 - 0.356: 13 0.356 - 0.445: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CB VAL A 283 " pdb=" CA VAL A 283 " pdb=" CG1 VAL A 283 " pdb=" CG2 VAL A 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CB VAL B 8 " pdb=" CA VAL B 8 " pdb=" CG1 VAL B 8 " pdb=" CG2 VAL B 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASP D 83 " pdb=" N ASP D 83 " pdb=" C ASP D 83 " pdb=" CB ASP D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 757 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG A 174 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 90 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 90 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 90 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 90 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 90 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 515 " 0.778 9.50e-02 1.11e+02 3.49e-01 7.39e+01 pdb=" NE ARG A 515 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 515 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 515 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 515 " 0.025 2.00e-02 2.50e+03 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1713 2.86 - 3.37: 4633 3.37 - 3.88: 8754 3.88 - 4.39: 10472 4.39 - 4.90: 16641 Nonbonded interactions: 42213 Sorted by model distance: nonbonded pdb=" O VAL A 414 " pdb=" OG1 THR A 418 " model vdw 2.347 3.040 nonbonded pdb=" OG SER B 20 " pdb=" O ASN B 87 " model vdw 2.381 3.040 nonbonded pdb=" N PHE B 30 " pdb=" O PHE B 30 " model vdw 2.407 2.496 nonbonded pdb=" N PHE B 107 " pdb=" O PHE B 107 " model vdw 2.414 2.496 nonbonded pdb=" O ALA A 306 " pdb=" OH TYR A 454 " model vdw 2.425 3.040 ... (remaining 42208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.230 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.940 Find NCS groups from input model: 0.050 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.013 0.078 4924 Z= 0.857 Angle : 1.822 11.298 6700 Z= 1.331 Chirality : 0.100 0.445 760 Planarity : 0.030 0.454 822 Dihedral : 14.971 87.582 1694 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.67 % Allowed : 9.65 % Favored : 86.68 % Cbeta Deviations : 0.18 % 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: -2.36 (0.30), residues: 607 helix: -1.53 (0.24), residues: 345 sheet: -0.13 (0.59), residues: 77 loop : -1.90 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 122 HIS 0.014 0.002 HIS A 198 PHE 0.042 0.003 PHE D 99 TYR 0.036 0.003 TYR B 57 ARG 0.004 0.001 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.528 Fit side-chains REVERT: A 101 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 102 LYS cc_start: 0.7064 (tttt) cc_final: 0.6563 (tttm) REVERT: A 300 LYS cc_start: 0.7833 (tttp) cc_final: 0.7614 (tttp) REVERT: A 365 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 371 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7472 (mtt180) REVERT: A 393 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6370 (tttt) outliers start: 19 outliers final: 4 residues processed: 99 average time/residue: 1.0587 time to fit residues: 109.5483 Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 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 127 GLN A 133 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 332 ASN A 368 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 520 ASN B 85 GLN D 38 GLN D 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4924 Z= 0.238 Angle : 0.606 7.741 6700 Z= 0.326 Chirality : 0.043 0.168 760 Planarity : 0.005 0.041 822 Dihedral : 5.480 44.872 673 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.32 % Allowed : 12.55 % Favored : 85.14 % 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: 0.18 (0.31), residues: 607 helix: 0.88 (0.26), residues: 344 sheet: 0.58 (0.59), residues: 72 loop : -1.40 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 228 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.002 PHE A 495 TYR 0.027 0.002 TYR A 117 ARG 0.005 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.564 Fit side-chains REVERT: A 102 LYS cc_start: 0.7076 (tttt) cc_final: 0.6475 (tttm) REVERT: A 169 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 305 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.7091 (ttt90) REVERT: A 365 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 371 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7391 (mtt180) REVERT: A 393 LYS cc_start: 0.6998 (ttpt) cc_final: 0.6308 (tttm) REVERT: A 420 ASN cc_start: 0.7657 (p0) cc_final: 0.7410 (p0) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 1.1120 time to fit residues: 78.0566 Evaluate side-chains 64 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 330 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4924 Z= 0.243 Angle : 0.567 7.725 6700 Z= 0.305 Chirality : 0.043 0.174 760 Planarity : 0.005 0.041 822 Dihedral : 5.014 46.162 666 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 12.55 % Favored : 84.75 % 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: 1.10 (0.32), residues: 607 helix: 1.62 (0.26), residues: 345 sheet: 0.77 (0.60), residues: 75 loop : -0.93 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.003 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.029 0.002 TYR A 117 ARG 0.003 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.543 Fit side-chains REVERT: A 102 LYS cc_start: 0.7073 (tttt) cc_final: 0.6465 (tttm) REVERT: A 155 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 223 ARG cc_start: 0.8219 (tpt170) cc_final: 0.8010 (tpt90) REVERT: A 365 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 371 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7479 (mtt180) REVERT: A 393 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6413 (tttm) REVERT: A 420 ASN cc_start: 0.7566 (p0) cc_final: 0.7294 (p0) outliers start: 14 outliers final: 5 residues processed: 64 average time/residue: 1.1343 time to fit residues: 75.9168 Evaluate side-chains 58 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.199 Angle : 0.524 7.120 6700 Z= 0.280 Chirality : 0.042 0.173 760 Planarity : 0.005 0.038 822 Dihedral : 4.798 45.446 666 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.90 % Allowed : 12.93 % Favored : 84.17 % 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: 1.60 (0.33), residues: 607 helix: 1.97 (0.26), residues: 346 sheet: 0.98 (0.60), residues: 75 loop : -0.63 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.028 0.001 TYR A 117 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.529 Fit side-chains REVERT: A 102 LYS cc_start: 0.7107 (tttt) cc_final: 0.6481 (tttm) REVERT: A 223 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7943 (tpt90) REVERT: A 371 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7446 (mtm180) REVERT: A 393 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6366 (tttm) REVERT: A 419 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 420 ASN cc_start: 0.7543 (p0) cc_final: 0.7267 (p0) REVERT: B 119 MET cc_start: 0.8387 (mtt) cc_final: 0.8127 (mtt) outliers start: 15 outliers final: 4 residues processed: 55 average time/residue: 1.1147 time to fit residues: 64.2456 Evaluate side-chains 52 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.201 Angle : 0.519 7.141 6700 Z= 0.277 Chirality : 0.042 0.175 760 Planarity : 0.005 0.038 822 Dihedral : 4.722 46.323 666 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.47 % Allowed : 12.55 % Favored : 83.98 % 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: 1.93 (0.33), residues: 607 helix: 2.14 (0.26), residues: 346 sheet: 1.23 (0.61), residues: 75 loop : -0.35 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.028 0.001 TYR A 117 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.545 Fit side-chains REVERT: A 102 LYS cc_start: 0.7119 (tttt) cc_final: 0.6558 (ttpp) REVERT: A 155 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 371 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7419 (mtm180) REVERT: A 393 LYS cc_start: 0.7084 (ttpt) cc_final: 0.6373 (tttm) REVERT: A 420 ASN cc_start: 0.7548 (p0) cc_final: 0.7276 (p0) REVERT: B 119 MET cc_start: 0.8378 (mtt) cc_final: 0.8111 (mtt) outliers start: 18 outliers final: 6 residues processed: 59 average time/residue: 1.1082 time to fit residues: 68.4947 Evaluate side-chains 56 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 361 HIS A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4924 Z= 0.237 Angle : 0.540 7.033 6700 Z= 0.287 Chirality : 0.043 0.181 760 Planarity : 0.005 0.039 822 Dihedral : 4.816 47.419 666 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.70 % Allowed : 13.32 % Favored : 83.98 % 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: 1.94 (0.33), residues: 607 helix: 2.04 (0.26), residues: 348 sheet: 1.38 (0.62), residues: 75 loop : -0.18 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.029 0.002 TYR A 117 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.554 Fit side-chains REVERT: A 102 LYS cc_start: 0.7140 (tttt) cc_final: 0.6534 (tttm) REVERT: A 155 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 371 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7402 (mtm180) REVERT: A 393 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6503 (tttm) REVERT: B 119 MET cc_start: 0.8366 (mtt) cc_final: 0.8079 (mtt) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 1.2269 time to fit residues: 70.4774 Evaluate side-chains 55 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN A 482 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.185 Angle : 0.511 6.803 6700 Z= 0.271 Chirality : 0.041 0.173 760 Planarity : 0.004 0.038 822 Dihedral : 4.647 45.656 666 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.90 % Allowed : 13.90 % Favored : 83.20 % 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: 2.19 (0.33), residues: 607 helix: 2.29 (0.26), residues: 344 sheet: 1.49 (0.62), residues: 75 loop : -0.15 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.027 0.001 TYR A 117 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.526 Fit side-chains REVERT: A 102 LYS cc_start: 0.7134 (tttt) cc_final: 0.6546 (tttm) REVERT: A 371 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7446 (mtm180) REVERT: A 393 LYS cc_start: 0.7119 (ttpt) cc_final: 0.6412 (tttm) REVERT: B 32 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 119 MET cc_start: 0.8346 (mtt) cc_final: 0.8100 (mtt) outliers start: 15 outliers final: 6 residues processed: 55 average time/residue: 1.1349 time to fit residues: 65.4081 Evaluate side-chains 55 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4924 Z= 0.230 Angle : 0.535 6.995 6700 Z= 0.283 Chirality : 0.042 0.180 760 Planarity : 0.005 0.039 822 Dihedral : 4.749 47.195 666 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.12 % Allowed : 14.09 % Favored : 83.78 % 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: 2.10 (0.33), residues: 607 helix: 2.13 (0.26), residues: 348 sheet: 1.59 (0.63), residues: 75 loop : -0.09 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.028 0.002 TYR A 117 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.679 Fit side-chains REVERT: A 102 LYS cc_start: 0.7159 (tttt) cc_final: 0.6546 (tttm) REVERT: A 371 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7409 (mtm180) REVERT: A 393 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6435 (tttm) REVERT: B 86 MET cc_start: 0.7191 (mtm) cc_final: 0.6896 (mtp) REVERT: B 119 MET cc_start: 0.8340 (mtt) cc_final: 0.8042 (mtt) outliers start: 11 outliers final: 6 residues processed: 51 average time/residue: 1.2366 time to fit residues: 66.2515 Evaluate side-chains 54 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4924 Z= 0.226 Angle : 0.535 6.881 6700 Z= 0.283 Chirality : 0.042 0.179 760 Planarity : 0.005 0.039 822 Dihedral : 4.745 47.123 666 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % 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: 2.15 (0.33), residues: 607 helix: 2.20 (0.26), residues: 344 sheet: 1.57 (0.63), residues: 75 loop : -0.08 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.028 0.002 TYR A 117 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.482 Fit side-chains REVERT: A 102 LYS cc_start: 0.7155 (tttt) cc_final: 0.6574 (tttm) REVERT: A 371 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7406 (mtm180) REVERT: A 393 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6449 (tttm) REVERT: A 420 ASN cc_start: 0.7423 (p0) cc_final: 0.7115 (p0) REVERT: B 119 MET cc_start: 0.8338 (mtt) cc_final: 0.8037 (mtt) outliers start: 14 outliers final: 7 residues processed: 52 average time/residue: 1.4931 time to fit residues: 81.2181 Evaluate side-chains 54 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 422 ASN A 470 GLN A 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.180 Angle : 0.510 6.584 6700 Z= 0.269 Chirality : 0.041 0.171 760 Planarity : 0.004 0.038 822 Dihedral : 4.562 45.078 666 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.74 % Allowed : 14.48 % Favored : 83.78 % 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: 2.35 (0.34), residues: 607 helix: 2.38 (0.26), residues: 347 sheet: 1.59 (0.63), residues: 75 loop : -0.04 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.027 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.471 Fit side-chains REVERT: A 102 LYS cc_start: 0.7178 (tttt) cc_final: 0.6571 (tttm) REVERT: A 371 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7448 (mtm180) REVERT: A 393 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6430 (tttm) REVERT: A 420 ASN cc_start: 0.7315 (p0) cc_final: 0.7006 (p0) REVERT: B 86 MET cc_start: 0.7141 (mtm) cc_final: 0.6930 (mtt) REVERT: B 119 MET cc_start: 0.8342 (mtt) cc_final: 0.8094 (mtt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 1.3642 time to fit residues: 71.1303 Evaluate side-chains 52 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118312 restraints weight = 4757.283| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.71 r_work: 0.3193 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4924 Z= 0.320 Angle : 0.589 7.295 6700 Z= 0.311 Chirality : 0.045 0.186 760 Planarity : 0.005 0.040 822 Dihedral : 4.970 49.610 666 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.74 % Allowed : 14.48 % Favored : 83.78 % 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: 1.92 (0.33), residues: 607 helix: 1.92 (0.26), residues: 348 sheet: 1.58 (0.63), residues: 75 loop : -0.05 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS A 272 PHE 0.020 0.002 PHE A 495 TYR 0.030 0.002 TYR A 117 ARG 0.003 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.51 seconds wall clock time: 37 minutes 42.35 seconds (2262.35 seconds total)