Starting phenix.real_space_refine on Mon Sep 23 14:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/09_2024/6jnd_9848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/09_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_9848/09_2024/6jnd_9848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/09_2024/6jnd_9848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/09_2024/6jnd_9848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/09_2024/6jnd_9848.cif" } 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. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3286 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398} 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 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.80 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 - 3.00 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: 0.90 Conformation dependent library (CDL) restraints added in 437.1 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... Secondary structure from input PDB file: 16 helices and 3 sheets defined 48.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 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 79 through 95 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 111 through 115 removed outlier: 3.943A pdb=" N LEU A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 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) removed outlier: 3.685A pdb=" N ARG A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.629A pdb=" N ILE A 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 165 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) removed outlier: 3.586A pdb=" N ARG A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.540A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.572A pdb=" N THR A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 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) removed outlier: 3.637A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.549A pdb=" N LEU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 286' Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 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 365 through 392 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 394 through 412 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=AA1, 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=AA2, first strand: chain 'A' and resid 68 through 69 removed outlier: 6.798A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.420A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 1.01 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: 0.00 - 1.38: 4153 1.38 - 2.76: 363 2.76 - 4.14: 34 4.14 - 5.53: 11 5.53 - 6.91: 1 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: 1093 2.83 - 3.35: 2726 3.35 - 3.87: 5053 3.87 - 4.38: 5857 4.38 - 4.90: 10120 Nonbonded interactions: 24849 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OE1 GLU A 368 " model vdw 2.324 3.040 nonbonded pdb=" O2 TRS A 901 " pdb=" O3 TRS A 901 " model vdw 2.337 3.040 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.346 3.120 nonbonded pdb=" O ASP A 340 " pdb=" ND2 ASN A 344 " model vdw 2.357 3.120 ... (remaining 24844 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: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- 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= 0.384 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 : 0.381 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: 0.1597 time to fit residues: 21.3403 Evaluate side-chains 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2917 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= 0.142 Angle : 0.516 5.849 4562 Z= 0.279 Chirality : 0.045 0.177 497 Planarity : 0.005 0.044 584 Dihedral : 6.242 48.808 473 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 19.06 % Favored : 77.42 % 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: -3.95 (0.34), residues: 417 helix: -2.99 (0.26), residues: 189 sheet: -1.41 (0.71), residues: 52 loop : -2.38 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.001 HIS A 267 PHE 0.023 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 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8015 (tpp) cc_final: 0.7792 (mmm) REVERT: A 26 GLU cc_start: 0.7498 (pt0) cc_final: 0.6862 (tt0) REVERT: A 90 MET cc_start: 0.8395 (tpt) cc_final: 0.8085 (tpp) REVERT: A 132 TYR cc_start: 0.8526 (t80) cc_final: 0.6106 (p90) REVERT: A 189 THR cc_start: 0.7914 (p) cc_final: 0.7611 (t) REVERT: A 193 GLN cc_start: 0.7398 (tp40) cc_final: 0.6667 (tt0) REVERT: A 287 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5669 (tt) REVERT: A 307 ASP cc_start: 0.5194 (OUTLIER) cc_final: 0.4984 (t70) outliers start: 12 outliers final: 4 residues processed: 76 average time/residue: 0.1586 time to fit residues: 14.6171 Evaluate side-chains 57 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain A residue 307 ASP 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: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.0070 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 40.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8476 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3366 Z= 0.308 Angle : 0.608 5.233 4562 Z= 0.324 Chirality : 0.047 0.144 497 Planarity : 0.005 0.046 584 Dihedral : 6.164 45.335 463 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.81 % Allowed : 19.94 % 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: -2.96 (0.38), residues: 417 helix: -1.73 (0.36), residues: 179 sheet: -1.90 (0.62), residues: 62 loop : -2.07 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 63 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.002 PHE A 341 TYR 0.011 0.001 TYR A 132 ARG 0.010 0.001 ARG A 370 *********************** 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 61 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.392 Fit side-chains REVERT: A 118 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7302 (mpp80) REVERT: A 189 THR cc_start: 0.8247 (p) cc_final: 0.7636 (t) REVERT: A 193 GLN cc_start: 0.7768 (tp40) cc_final: 0.6582 (mt0) REVERT: A 220 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: A 304 LYS cc_start: 0.7037 (mttm) cc_final: 0.6133 (mmmt) REVERT: A 375 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8473 (tttt) REVERT: A 388 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7981 (t70) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.2082 time to fit residues: 14.5162 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3366 Z= 0.167 Angle : 0.504 8.964 4562 Z= 0.261 Chirality : 0.044 0.128 497 Planarity : 0.004 0.035 584 Dihedral : 5.292 38.461 461 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.93 % Allowed : 21.99 % Favored : 75.07 % 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: -2.30 (0.39), residues: 417 helix: -0.99 (0.37), residues: 183 sheet: -1.61 (0.65), residues: 62 loop : -1.95 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.001 0.000 HIS A 61 PHE 0.013 0.001 PHE A 341 TYR 0.010 0.001 TYR A 132 ARG 0.006 0.001 ARG A 370 *********************** 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 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.408 Fit side-chains REVERT: A 9 MET cc_start: 0.7790 (tpp) cc_final: 0.7435 (mmp) REVERT: A 90 MET cc_start: 0.8770 (tpt) cc_final: 0.8129 (tpt) REVERT: A 118 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7370 (mpp80) REVERT: A 189 THR cc_start: 0.8254 (p) cc_final: 0.7644 (t) REVERT: A 291 VAL cc_start: 0.8591 (m) cc_final: 0.8330 (m) REVERT: A 304 LYS cc_start: 0.7035 (mttm) cc_final: 0.6251 (mmmt) REVERT: A 336 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8891 (tt) REVERT: A 370 ARG cc_start: 0.8372 (ttt-90) cc_final: 0.7338 (ttm110) REVERT: A 388 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.8049 (t70) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1796 time to fit residues: 11.7135 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3366 Z= 0.266 Angle : 0.549 5.882 4562 Z= 0.291 Chirality : 0.047 0.143 497 Planarity : 0.004 0.035 584 Dihedral : 5.467 41.478 459 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.69 % Allowed : 21.70 % Favored : 73.61 % 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: -2.05 (0.40), residues: 417 helix: -0.71 (0.37), residues: 182 sheet: -1.77 (0.67), residues: 56 loop : -1.81 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 PHE 0.017 0.002 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.006 0.001 ARG A 370 *********************** 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 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.404 Fit side-chains REVERT: A 9 MET cc_start: 0.7880 (tpp) cc_final: 0.7564 (mmp) REVERT: A 118 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7502 (mpp80) REVERT: A 232 LYS cc_start: 0.7937 (tppt) cc_final: 0.7694 (ttpt) REVERT: A 375 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8482 (tttt) outliers start: 16 outliers final: 10 residues processed: 53 average time/residue: 0.1653 time to fit residues: 10.8552 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3366 Z= 0.348 Angle : 0.578 4.968 4562 Z= 0.308 Chirality : 0.049 0.165 497 Planarity : 0.004 0.034 584 Dihedral : 5.863 48.318 459 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.11 % Allowed : 22.29 % Favored : 73.61 % 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: -2.08 (0.40), residues: 417 helix: -0.69 (0.37), residues: 182 sheet: -1.46 (0.77), residues: 46 loop : -2.01 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.006 0.001 TYR A 408 ARG 0.004 0.001 ARG A 370 *********************** 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 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.492 Fit side-chains REVERT: A 9 MET cc_start: 0.7927 (tpp) cc_final: 0.7562 (mmp) REVERT: A 118 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7484 (mpp80) REVERT: A 375 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8510 (tttt) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1628 time to fit residues: 10.4947 Evaluate side-chains 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3366 Z= 0.152 Angle : 0.474 4.239 4562 Z= 0.250 Chirality : 0.045 0.140 497 Planarity : 0.004 0.034 584 Dihedral : 5.328 45.750 459 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.64 % Allowed : 24.34 % 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: -1.57 (0.41), residues: 417 helix: -0.18 (0.39), residues: 181 sheet: -1.51 (0.67), residues: 62 loop : -1.70 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.006 0.001 TYR A 132 ARG 0.004 0.000 ARG A 370 *********************** 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 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.372 Fit side-chains REVERT: A 9 MET cc_start: 0.7670 (tpp) cc_final: 0.7379 (mmp) REVERT: A 46 MET cc_start: 0.8890 (mmm) cc_final: 0.8521 (mmm) REVERT: A 90 MET cc_start: 0.8634 (tpt) cc_final: 0.8080 (tpt) REVERT: A 118 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7304 (mpp80) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1909 time to fit residues: 11.9175 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 307 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3366 Z= 0.263 Angle : 0.522 4.797 4562 Z= 0.276 Chirality : 0.047 0.144 497 Planarity : 0.004 0.035 584 Dihedral : 5.519 47.768 459 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.52 % Allowed : 23.17 % Favored : 73.31 % 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: -1.63 (0.41), residues: 417 helix: -0.25 (0.38), residues: 181 sheet: -1.57 (0.69), residues: 56 loop : -1.71 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.005 0.001 TYR A 132 ARG 0.004 0.000 ARG A 370 *********************** 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 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.381 Fit side-chains REVERT: A 9 MET cc_start: 0.7797 (tpp) cc_final: 0.7497 (mmp) REVERT: A 46 MET cc_start: 0.8907 (mmm) cc_final: 0.8555 (mmm) REVERT: A 118 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7299 (mpp80) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.1812 time to fit residues: 11.4953 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3366 Z= 0.130 Angle : 0.475 6.848 4562 Z= 0.250 Chirality : 0.043 0.149 497 Planarity : 0.004 0.038 584 Dihedral : 5.015 42.607 459 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.59 % Allowed : 26.69 % 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: -1.14 (0.41), residues: 417 helix: 0.17 (0.39), residues: 181 sheet: -1.20 (0.68), residues: 62 loop : -1.51 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.006 0.001 TYR A 220 ARG 0.004 0.000 ARG A 370 *********************** 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 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.391 Fit side-chains REVERT: A 90 MET cc_start: 0.8611 (tpt) cc_final: 0.8159 (tpt) REVERT: A 118 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7349 (mpp80) outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.1699 time to fit residues: 9.2623 Evaluate side-chains 41 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3366 Z= 0.217 Angle : 0.533 7.497 4562 Z= 0.276 Chirality : 0.046 0.217 497 Planarity : 0.004 0.036 584 Dihedral : 5.092 43.439 459 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.88 % Allowed : 26.39 % 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: -1.25 (0.41), residues: 417 helix: 0.10 (0.38), residues: 181 sheet: -1.18 (0.74), residues: 52 loop : -1.62 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.013 0.001 PHE A 381 TYR 0.005 0.001 TYR A 385 ARG 0.004 0.000 ARG A 370 ********************** 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 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.391 Fit side-chains REVERT: A 118 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7375 (mpp80) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1886 time to fit residues: 9.9552 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 2.9664 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088002 restraints weight = 5951.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088547 restraints weight = 4785.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088546 restraints weight = 4189.835| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3366 Z= 0.209 Angle : 0.519 6.113 4562 Z= 0.271 Chirality : 0.047 0.201 497 Planarity : 0.004 0.036 584 Dihedral : 5.108 43.715 459 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.17 % Allowed : 25.81 % 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: -1.20 (0.41), residues: 417 helix: 0.13 (0.38), residues: 181 sheet: -1.15 (0.75), residues: 52 loop : -1.59 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.006 0.001 TYR A 385 ARG 0.004 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1012.87 seconds wall clock time: 18 minutes 44.75 seconds (1124.75 seconds total)