Starting phenix.real_space_refine on Sun Mar 10 16:19:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/03_2024/6jnd_9848_updated.pdb" } resolution = 3.9 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= 0.002 sd= 0.013 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 15 5.16 5 C 2103 2.51 5 N 561 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3294 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3294 Unusual residues: {'TRS': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 419 "'] Classifications: {'peptide': 419, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398, None: 1} Not linked: pdbres="LYS A 419 " pdbres="TRS A 901 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.67 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.34, 73.08, 73.95, 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 15 16.00 O 615 8.00 N 561 7.00 C 2103 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: 1.27 Conformation dependent library (CDL) restraints added in 615.7 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 41.3% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.755A pdb=" N ALA A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.826A pdb=" N ALA A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.586A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.536A pdb=" N GLY A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 190 through 206 removed outlier: 3.572A pdb=" N THR A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.552A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.765A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 340 through 360 removed outlier: 4.769A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 391 removed outlier: 4.005A pdb=" N ASP A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 4.125A pdb=" N TYR A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 3.604A pdb=" N GLY A 107 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 3.733A pdb=" N VAL A 291 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 216 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 218 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) 96 hydrogen bonds defined for protein. 285 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: 0.81 Time building geometry restraints manager: 1.38 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: 1073 1.34 - 1.46: 611 1.46 - 1.57: 1653 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 3366 Sorted by residual: bond pdb=" N TRS A 901 " pdb=" C TRS A 901 " ideal model delta sigma weight residual 1.501 1.462 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C LYS A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.59e+00 bond pdb=" CB ASN A 62 " pdb=" CG ASN A 62 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CA ARG A 36 " pdb=" C ARG A 36 " ideal model delta sigma weight residual 1.529 1.516 0.013 1.04e-02 9.25e+03 1.52e+00 bond pdb=" CA ASP A 145 " pdb=" CB ASP A 145 " ideal model delta sigma weight residual 1.539 1.525 0.014 1.36e-02 5.41e+03 1.11e+00 ... (remaining 3361 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.86: 110 106.86 - 113.71: 1882 113.71 - 120.56: 1363 120.56 - 127.42: 1163 127.42 - 134.27: 44 Bond angle restraints: 4562 Sorted by residual: angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 113.20 106.29 6.91 9.60e-01 1.09e+00 5.18e+01 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.83 108.49 4.34 9.90e-01 1.02e+00 1.93e+01 angle pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 117.96 120.68 -2.72 8.10e-01 1.52e+00 1.13e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.68 -4.63 1.57e+00 4.06e-01 8.70e+00 angle pdb=" C LYS A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta sigma weight residual 122.40 126.57 -4.17 1.45e+00 4.76e-01 8.27e+00 ... (remaining 4557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1785 17.36 - 34.72: 165 34.72 - 52.07: 51 52.07 - 69.43: 10 69.43 - 86.79: 5 Dihedral angle restraints: 2016 sinusoidal: 818 harmonic: 1198 Sorted by residual: dihedral pdb=" CA TYR A 147 " pdb=" C TYR A 147 " pdb=" N THR A 148 " pdb=" CA THR A 148 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 266 0.034 - 0.068: 160 0.068 - 0.102: 41 0.102 - 0.136: 27 0.136 - 0.170: 3 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYR A 147 " pdb=" N TYR A 147 " pdb=" C TYR A 147 " pdb=" CB TYR A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 494 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 142 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 5 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO A 6 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 6 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 6 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 150 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.029 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1098 2.83 - 3.35: 2743 3.35 - 3.87: 5074 3.87 - 4.38: 5903 4.38 - 4.90: 10127 Nonbonded interactions: 24945 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.316 2.440 nonbonded pdb=" OG1 THR A 365 " pdb=" OE1 GLU A 368 " model vdw 2.324 2.440 nonbonded pdb=" O2 TRS A 901 " pdb=" O3 TRS A 901 " model vdw 2.337 2.440 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.346 2.520 nonbonded pdb=" O ASP A 340 " pdb=" ND2 ASN A 344 " model vdw 2.357 2.520 ... (remaining 24940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.460 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: 2.510 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.090 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3366 Z= 0.382 Angle : 0.825 6.907 4562 Z= 0.538 Chirality : 0.050 0.170 497 Planarity : 0.007 0.058 584 Dihedral : 15.637 86.791 1252 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 11.73 % Allowed : 11.14 % Favored : 77.13 % 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: -5.73 (0.30), residues: 417 helix: -4.79 (0.14), residues: 183 sheet: -2.24 (0.72), residues: 46 loop : -3.00 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 30 HIS 0.003 0.001 HIS A 61 PHE 0.011 0.001 PHE A 341 TYR 0.006 0.002 TYR A 160 ARG 0.003 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 78 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7330 (pt0) cc_final: 0.6688 (tt0) REVERT: A 90 MET cc_start: 0.8581 (tpt) cc_final: 0.7870 (tpt) REVERT: A 118 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7288 (mpp80) REVERT: A 189 THR cc_start: 0.7667 (p) cc_final: 0.7465 (t) REVERT: A 193 GLN cc_start: 0.7386 (tp40) cc_final: 0.6650 (tt0) REVERT: A 307 ASP cc_start: 0.5233 (OUTLIER) cc_final: 0.4767 (t70) REVERT: A 388 HIS cc_start: 0.7906 (t70) cc_final: 0.7548 (t70) outliers start: 40 outliers final: 8 residues processed: 110 average time/residue: 0.1542 time to fit residues: 20.5296 Evaluate side-chains 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3366 Z= 0.121 Angle : 0.484 6.280 4562 Z= 0.258 Chirality : 0.043 0.172 497 Planarity : 0.005 0.043 584 Dihedral : 5.556 35.182 473 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.52 % Allowed : 20.23 % Favored : 76.25 % 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: -3.86 (0.35), residues: 417 helix: -3.23 (0.26), residues: 178 sheet: -1.83 (0.67), residues: 56 loop : -1.88 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 89 HIS 0.003 0.001 HIS A 267 PHE 0.024 0.002 PHE A 273 TYR 0.019 0.001 TYR A 132 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7371 (pt0) cc_final: 0.6779 (tt0) REVERT: A 90 MET cc_start: 0.8385 (tpt) cc_final: 0.7837 (tpt) REVERT: A 132 TYR cc_start: 0.8439 (t80) cc_final: 0.6094 (p90) REVERT: A 189 THR cc_start: 0.7564 (p) cc_final: 0.7325 (t) REVERT: A 370 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7066 (tpp-160) outliers start: 12 outliers final: 5 residues processed: 77 average time/residue: 0.1499 time to fit residues: 14.2876 Evaluate side-chains 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 193 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 394 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3366 Z= 0.316 Angle : 0.613 6.254 4562 Z= 0.323 Chirality : 0.047 0.148 497 Planarity : 0.005 0.045 584 Dihedral : 5.527 29.416 463 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.69 % Allowed : 19.65 % Favored : 75.66 % 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: -2.93 (0.38), residues: 417 helix: -1.94 (0.36), residues: 172 sheet: -1.85 (0.65), residues: 56 loop : -1.83 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 63 HIS 0.003 0.001 HIS A 394 PHE 0.020 0.002 PHE A 381 TYR 0.013 0.001 TYR A 132 ARG 0.005 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.402 Fit side-chains REVERT: A 90 MET cc_start: 0.8934 (tpt) cc_final: 0.8192 (tpt) REVERT: A 118 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7354 (mpp80) REVERT: A 189 THR cc_start: 0.8178 (p) cc_final: 0.7781 (t) REVERT: A 284 LEU cc_start: 0.8413 (tt) cc_final: 0.7979 (tp) REVERT: A 304 LYS cc_start: 0.7136 (mttm) cc_final: 0.6341 (mmtt) REVERT: A 348 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (t) REVERT: A 370 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7297 (ttm110) REVERT: A 375 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8473 (tttt) REVERT: A 409 GLN cc_start: 0.9124 (tp40) cc_final: 0.8672 (tp40) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.2002 time to fit residues: 13.6660 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 397 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3366 Z= 0.234 Angle : 0.504 5.218 4562 Z= 0.262 Chirality : 0.045 0.126 497 Planarity : 0.004 0.035 584 Dihedral : 5.002 32.960 461 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.52 % Allowed : 22.29 % Favored : 74.19 % 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: -2.27 (0.40), residues: 417 helix: -1.21 (0.38), residues: 173 sheet: -1.97 (0.62), residues: 61 loop : -1.46 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 155 HIS 0.002 0.001 HIS A 394 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 132 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.398 Fit side-chains REVERT: A 90 MET cc_start: 0.8820 (tpt) cc_final: 0.8251 (tpt) REVERT: A 118 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7500 (mpp80) REVERT: A 189 THR cc_start: 0.8198 (p) cc_final: 0.7745 (t) REVERT: A 304 LYS cc_start: 0.7099 (mttm) cc_final: 0.6281 (mmmt) REVERT: A 348 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8669 (t) REVERT: A 370 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7266 (ttm110) outliers start: 12 outliers final: 6 residues processed: 52 average time/residue: 0.1884 time to fit residues: 11.8813 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 30.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3366 Z= 0.148 Angle : 0.451 5.604 4562 Z= 0.229 Chirality : 0.043 0.124 497 Planarity : 0.004 0.034 584 Dihedral : 4.324 35.181 458 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.11 % Allowed : 22.87 % Favored : 73.02 % 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: -1.77 (0.41), residues: 417 helix: -0.58 (0.40), residues: 175 sheet: -1.62 (0.65), residues: 61 loop : -1.48 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 394 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 132 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.367 Fit side-chains REVERT: A 118 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7518 (mpp80) REVERT: A 304 LYS cc_start: 0.7230 (mttm) cc_final: 0.6330 (mtpt) REVERT: A 370 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7161 (tpp-160) REVERT: A 375 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (tttt) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 0.1710 time to fit residues: 11.4810 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3366 Z= 0.146 Angle : 0.484 9.427 4562 Z= 0.238 Chirality : 0.043 0.124 497 Planarity : 0.004 0.036 584 Dihedral : 4.238 36.385 458 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 24.63 % Favored : 72.73 % 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: -1.40 (0.41), residues: 417 helix: -0.25 (0.40), residues: 174 sheet: -1.41 (0.68), residues: 61 loop : -1.33 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 394 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.397 Fit side-chains REVERT: A 118 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7336 (mpp80) REVERT: A 157 MET cc_start: 0.8739 (tmm) cc_final: 0.8501 (tmm) REVERT: A 304 LYS cc_start: 0.7297 (mttm) cc_final: 0.6380 (mmmt) REVERT: A 370 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7131 (tpp-160) REVERT: A 375 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8477 (tttt) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1763 time to fit residues: 10.7441 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.0270 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 357 GLN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3366 Z= 0.119 Angle : 0.451 7.396 4562 Z= 0.226 Chirality : 0.043 0.121 497 Planarity : 0.003 0.037 584 Dihedral : 4.073 37.633 458 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.76 % Allowed : 25.22 % Favored : 73.02 % 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: -1.01 (0.42), residues: 417 helix: 0.14 (0.41), residues: 174 sheet: -1.21 (0.69), residues: 61 loop : -1.18 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.006 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 132 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.392 Fit side-chains REVERT: A 118 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7337 (mpp80) REVERT: A 157 MET cc_start: 0.8723 (tmm) cc_final: 0.8511 (tmm) REVERT: A 304 LYS cc_start: 0.7296 (mttm) cc_final: 0.6331 (mmmt) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.1727 time to fit residues: 11.2010 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.0270 chunk 34 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3366 Z= 0.223 Angle : 0.504 6.591 4562 Z= 0.257 Chirality : 0.046 0.205 497 Planarity : 0.004 0.035 584 Dihedral : 4.526 37.694 458 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.64 % Allowed : 25.51 % Favored : 71.85 % 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: -1.04 (0.42), residues: 417 helix: 0.11 (0.41), residues: 174 sheet: -1.25 (0.69), residues: 61 loop : -1.17 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.005 0.001 HIS A 394 PHE 0.013 0.001 PHE A 381 TYR 0.005 0.001 TYR A 408 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.427 Fit side-chains REVERT: A 118 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7383 (mpp80) REVERT: A 370 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7189 (tpp-160) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1827 time to fit residues: 10.7386 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.7600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3366 Z= 0.144 Angle : 0.469 6.887 4562 Z= 0.236 Chirality : 0.044 0.182 497 Planarity : 0.004 0.038 584 Dihedral : 4.229 38.363 458 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.35 % Allowed : 25.22 % Favored : 72.43 % 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: -0.85 (0.42), residues: 417 helix: 0.30 (0.41), residues: 173 sheet: -1.13 (0.69), residues: 61 loop : -1.10 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.007 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.005 0.001 TYR A 132 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.400 Fit side-chains REVERT: A 118 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7368 (mpp80) REVERT: A 370 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7137 (tpp-160) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.1814 time to fit residues: 10.4229 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 394 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.7698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3366 Z= 0.178 Angle : 0.476 6.169 4562 Z= 0.243 Chirality : 0.045 0.179 497 Planarity : 0.004 0.039 584 Dihedral : 4.284 38.386 458 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.64 % Allowed : 25.51 % Favored : 71.85 % 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: 417 helix: 0.32 (0.41), residues: 173 sheet: -1.22 (0.68), residues: 61 loop : -1.05 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.007 0.001 HIS A 394 PHE 0.011 0.001 PHE A 381 TYR 0.005 0.001 TYR A 132 ARG 0.002 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.401 Fit side-chains REVERT: A 118 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7372 (mpp80) REVERT: A 267 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7636 (t70) REVERT: A 370 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7120 (tpp-160) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1829 time to fit residues: 10.7713 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086590 restraints weight = 5910.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087281 restraints weight = 4842.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087561 restraints weight = 4269.046| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3366 Z= 0.257 Angle : 0.522 6.364 4562 Z= 0.270 Chirality : 0.047 0.171 497 Planarity : 0.004 0.038 584 Dihedral : 4.685 37.596 458 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.64 % Allowed : 25.81 % Favored : 71.55 % 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: -1.01 (0.42), residues: 417 helix: 0.13 (0.41), residues: 174 sheet: -1.42 (0.66), residues: 61 loop : -1.07 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.014 0.002 PHE A 381 TYR 0.005 0.001 TYR A 408 ARG 0.002 0.000 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.68 seconds wall clock time: 18 minutes 58.48 seconds (1138.48 seconds total)