Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:18:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/04_2023/6jnd_9848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/04_2023/6jnd_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_9848/04_2023/6jnd_9848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/04_2023/6jnd_9848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/04_2023/6jnd_9848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnd_9848/04_2023/6jnd_9848_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 2.27, per 1000 atoms: 0.69 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: 1.23 Conformation dependent library (CDL) restraints added in 493.9 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: 0.35 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: 0.75 Time building geometry restraints manager: 1.35 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: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.600 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.100 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.356 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 8 residues processed: 110 average time/residue: 0.1414 time to fit residues: 18.9025 Evaluate side-chains 60 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0337 time to fit residues: 0.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 9.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3366 Z= 0.124 Angle : 0.488 6.217 4562 Z= 0.260 Chirality : 0.043 0.161 497 Planarity : 0.005 0.043 584 Dihedral : 4.468 19.777 458 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.64 % 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: -3.83 (0.35), residues: 417 helix: -3.18 (0.26), residues: 177 sheet: -1.81 (0.68), residues: 56 loop : -1.90 (0.44), residues: 184 *********************** 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 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.1536 time to fit residues: 13.8957 Evaluate side-chains 52 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1068 time to fit residues: 1.0968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3366 Z= 0.214 Angle : 0.543 6.388 4562 Z= 0.284 Chirality : 0.045 0.135 497 Planarity : 0.005 0.045 584 Dihedral : 4.555 22.309 458 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.64 % 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: -2.65 (0.38), residues: 417 helix: -1.62 (0.37), residues: 171 sheet: -1.56 (0.66), residues: 54 loop : -1.83 (0.42), residues: 192 *********************** 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 55 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.357 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.1709 time to fit residues: 11.1488 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0697 time to fit residues: 1.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6331 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= 0.206 Angle : 0.502 5.782 4562 Z= 0.259 Chirality : 0.045 0.125 497 Planarity : 0.004 0.034 584 Dihedral : 4.444 24.672 458 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.40), residues: 417 helix: -1.00 (0.39), residues: 172 sheet: -1.80 (0.63), residues: 61 loop : -1.30 (0.46), residues: 184 *********************** 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.358 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.1912 time to fit residues: 9.5912 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0525 time to fit residues: 0.6681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 40.0000 chunk 16 optimal weight: 0.0270 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 overall best weight: 2.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.6865 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= 0.188 Angle : 0.473 5.838 4562 Z= 0.242 Chirality : 0.045 0.125 497 Planarity : 0.004 0.034 584 Dihedral : 4.356 25.005 458 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.76 % 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: -1.67 (0.41), residues: 417 helix: -0.52 (0.40), residues: 172 sheet: -1.76 (0.64), residues: 61 loop : -1.31 (0.46), residues: 184 *********************** 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.1571 time to fit residues: 8.4960 Evaluate side-chains 35 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0382 time to fit residues: 0.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 39 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 3366 Z= 0.130 Angle : 0.501 11.468 4562 Z= 0.241 Chirality : 0.043 0.120 497 Planarity : 0.003 0.036 584 Dihedral : 4.022 24.985 458 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.41), residues: 417 helix: -0.08 (0.40), residues: 173 sheet: -1.37 (0.68), residues: 61 loop : -1.20 (0.44), residues: 183 *********************** 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 37 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.420 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1693 time to fit residues: 8.0670 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0444 time to fit residues: 0.7442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 8.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3366 Z= 0.230 Angle : 0.545 8.722 4562 Z= 0.268 Chirality : 0.046 0.129 497 Planarity : 0.004 0.034 584 Dihedral : 4.486 25.944 458 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.05 % 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: 0.04 (0.40), residues: 170 sheet: -1.52 (0.68), residues: 61 loop : -1.24 (0.45), residues: 186 *********************** 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 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.398 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.1577 time to fit residues: 8.6297 Evaluate side-chains 39 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0351 time to fit residues: 0.7304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3366 Z= 0.152 Angle : 0.498 8.378 4562 Z= 0.243 Chirality : 0.044 0.121 497 Planarity : 0.003 0.037 584 Dihedral : 4.098 24.433 458 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 417 helix: 0.27 (0.40), residues: 171 sheet: -1.32 (0.69), residues: 61 loop : -1.13 (0.45), residues: 185 *********************** 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 38 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.427 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1695 time to fit residues: 8.2146 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8405 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3366 Z= 0.116 Angle : 0.460 7.797 4562 Z= 0.226 Chirality : 0.042 0.121 497 Planarity : 0.003 0.039 584 Dihedral : 3.714 24.074 458 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.42), residues: 417 helix: 0.61 (0.41), residues: 171 sheet: -0.79 (0.75), residues: 56 loop : -1.16 (0.44), residues: 190 *********************** 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 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.449 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1774 time to fit residues: 9.2594 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3366 Z= 0.140 Angle : 0.498 9.957 4562 Z= 0.243 Chirality : 0.044 0.203 497 Planarity : 0.003 0.039 584 Dihedral : 3.789 23.845 458 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.42), residues: 417 helix: 0.67 (0.41), residues: 171 sheet: -1.11 (0.70), residues: 61 loop : -0.95 (0.45), residues: 185 ********************** 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 38 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1653 time to fit residues: 8.0118 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.092116 restraints weight = 6008.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093173 restraints weight = 4540.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093921 restraints weight = 3800.491| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.7939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3366 Z= 0.226 Angle : 0.543 9.744 4562 Z= 0.269 Chirality : 0.046 0.176 497 Planarity : 0.004 0.036 584 Dihedral : 4.316 27.558 458 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.41), residues: 417 helix: 0.22 (0.40), residues: 176 sheet: -1.28 (0.68), residues: 61 loop : -1.06 (0.47), residues: 180 =============================================================================== Job complete usr+sys time: 970.41 seconds wall clock time: 18 minutes 18.59 seconds (1098.59 seconds total)