Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 17:32:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/07_2023/7xpz_33386.pdb" } resolution = 3.4 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= 0.000 sd= 0.003 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 10 5.16 5 C 2148 2.51 5 N 530 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3227 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3227 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 1.97, per 1000 atoms: 0.61 Number of scatterers: 3227 At special positions: 0 Unit cell: (81, 75, 63, 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 10 16.00 O 539 8.00 N 530 7.00 C 2148 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: 1.26 Conformation dependent library (CDL) restraints added in 472.6 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.576A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.550A pdb=" N THR A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.672A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.937A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.540A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.623A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.340A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.820A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.577A pdb=" N ALA A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.735A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.642A pdb=" N SER A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.600A pdb=" N ASN A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.919A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.853A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.915A pdb=" N THR A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.594A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.881A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.868A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 480 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: 0.78 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 962 1.34 - 1.46: 827 1.46 - 1.57: 1511 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3316 Sorted by residual: bond pdb=" C THR A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" CB PRO A 70 " pdb=" CG PRO A 70 " ideal model delta sigma weight residual 1.492 1.437 0.055 5.00e-02 4.00e+02 1.19e+00 bond pdb=" CB PRO A 381 " pdb=" CG PRO A 381 " ideal model delta sigma weight residual 1.492 1.439 0.053 5.00e-02 4.00e+02 1.11e+00 bond pdb=" CB PRO A 94 " pdb=" CG PRO A 94 " ideal model delta sigma weight residual 1.492 1.440 0.052 5.00e-02 4.00e+02 1.08e+00 bond pdb=" CB PRO A 50 " pdb=" CG PRO A 50 " ideal model delta sigma weight residual 1.492 1.443 0.049 5.00e-02 4.00e+02 9.47e-01 ... (remaining 3311 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 79 106.84 - 113.63: 1818 113.63 - 120.41: 1440 120.41 - 127.20: 1143 127.20 - 133.99: 40 Bond angle restraints: 4520 Sorted by residual: angle pdb=" C VAL A 250 " pdb=" N LEU A 251 " pdb=" CA LEU A 251 " ideal model delta sigma weight residual 123.05 128.86 -5.81 1.57e+00 4.06e-01 1.37e+01 angle pdb=" N ALA A 252 " pdb=" CA ALA A 252 " pdb=" C ALA A 252 " ideal model delta sigma weight residual 113.18 108.52 4.66 1.33e+00 5.65e-01 1.23e+01 angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 110.80 117.03 -6.23 2.13e+00 2.20e-01 8.57e+00 angle pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N PRO A 70 " ideal model delta sigma weight residual 118.44 122.92 -4.48 1.59e+00 3.96e-01 7.94e+00 angle pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta sigma weight residual 121.54 116.19 5.35 1.91e+00 2.74e-01 7.85e+00 ... (remaining 4515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 1743 15.48 - 30.95: 132 30.95 - 46.42: 27 46.42 - 61.90: 6 61.90 - 77.37: 2 Dihedral angle restraints: 1910 sinusoidal: 725 harmonic: 1185 Sorted by residual: dihedral pdb=" CA ASN A 300 " pdb=" C ASN A 300 " pdb=" N SER A 301 " pdb=" CA SER A 301 " ideal model delta harmonic sigma weight residual 180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA THR A 298 " pdb=" C THR A 298 " pdb=" N THR A 299 " pdb=" CA THR A 299 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 302 0.037 - 0.073: 170 0.073 - 0.110: 46 0.110 - 0.146: 8 0.146 - 0.183: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 525 not shown) Planarity restraints: 546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 82 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO A 70 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 380 " -0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 381 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.040 5.00e-02 4.00e+02 ... (remaining 543 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1104 2.83 - 3.35: 2879 3.35 - 3.86: 5331 3.86 - 4.38: 6586 4.38 - 4.90: 10693 Nonbonded interactions: 26593 Sorted by model distance: nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.311 2.440 nonbonded pdb=" O THR A 404 " pdb=" OG1 THR A 408 " model vdw 2.319 2.440 nonbonded pdb=" OD2 ASP A 56 " pdb=" OG SER A 183 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.334 2.440 nonbonded pdb=" OG SER A 271 " pdb=" OD1 ASN A 403 " model vdw 2.337 2.440 ... (remaining 26588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.090 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.005 0.055 3316 Z= 0.343 Angle : 0.732 6.979 4520 Z= 0.426 Chirality : 0.046 0.183 528 Planarity : 0.008 0.075 546 Dihedral : 12.260 77.370 1148 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.77 (0.22), residues: 398 helix: -4.54 (0.11), residues: 308 sheet: None (None), residues: 0 loop : -2.98 (0.52), residues: 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.367 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.1877 time to fit residues: 12.8096 Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0483 time to fit residues: 0.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 431 GLN A 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3316 Z= 0.200 Angle : 0.567 6.187 4520 Z= 0.298 Chirality : 0.038 0.116 528 Planarity : 0.005 0.044 546 Dihedral : 5.157 21.453 449 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 2.31 % 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: -4.62 (0.32), residues: 398 helix: -2.97 (0.21), residues: 310 sheet: None (None), residues: 0 loop : -2.34 (0.58), residues: 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.369 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.1218 time to fit residues: 8.0749 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0364 time to fit residues: 0.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3316 Z= 0.176 Angle : 0.532 6.263 4520 Z= 0.271 Chirality : 0.037 0.116 528 Planarity : 0.004 0.031 546 Dihedral : 4.783 19.253 449 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.73 % 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: -2.99 (0.37), residues: 398 helix: -1.78 (0.26), residues: 310 sheet: None (None), residues: 0 loop : -1.92 (0.62), residues: 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.327 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.1140 time to fit residues: 6.9661 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0456 time to fit residues: 0.7725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3316 Z= 0.176 Angle : 0.512 6.460 4520 Z= 0.261 Chirality : 0.037 0.117 528 Planarity : 0.003 0.027 546 Dihedral : 4.614 18.106 449 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.40), residues: 398 helix: -1.18 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.85 (0.65), residues: 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.348 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.0865 time to fit residues: 5.6046 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0423 time to fit residues: 0.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3316 Z= 0.260 Angle : 0.563 6.645 4520 Z= 0.281 Chirality : 0.040 0.124 528 Planarity : 0.003 0.026 546 Dihedral : 4.635 17.713 449 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.15 % 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: -1.84 (0.41), residues: 398 helix: -0.92 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.69 (0.67), residues: 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.381 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 0.1247 time to fit residues: 7.9902 Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3316 Z= 0.186 Angle : 0.525 6.401 4520 Z= 0.264 Chirality : 0.038 0.118 528 Planarity : 0.003 0.024 546 Dihedral : 4.506 16.907 449 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.42), residues: 398 helix: -0.60 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.60 (0.67), residues: 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.346 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.0928 time to fit residues: 6.0550 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0356 time to fit residues: 0.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3316 Z= 0.230 Angle : 0.556 6.767 4520 Z= 0.275 Chirality : 0.039 0.121 528 Planarity : 0.003 0.024 546 Dihedral : 4.499 17.009 449 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: -1.22 (0.42), residues: 398 helix: -0.50 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.41 (0.70), residues: 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.328 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1209 time to fit residues: 6.9103 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3316 Z= 0.208 Angle : 0.569 6.666 4520 Z= 0.283 Chirality : 0.039 0.119 528 Planarity : 0.003 0.024 546 Dihedral : 4.470 16.774 449 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -1.06 (0.43), residues: 398 helix: -0.38 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.37 (0.71), residues: 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1293 time to fit residues: 7.0402 Evaluate side-chains 40 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3316 Z= 0.229 Angle : 0.579 6.662 4520 Z= 0.283 Chirality : 0.039 0.121 528 Planarity : 0.003 0.024 546 Dihedral : 4.467 16.627 449 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.15 % 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: -0.96 (0.43), residues: 398 helix: -0.32 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.33 (0.72), residues: 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.337 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1242 time to fit residues: 6.9030 Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0342 time to fit residues: 0.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3316 Z= 0.187 Angle : 0.581 8.311 4520 Z= 0.283 Chirality : 0.038 0.118 528 Planarity : 0.003 0.024 546 Dihedral : 4.426 16.224 449 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -0.85 (0.43), residues: 398 helix: -0.22 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.37 (0.72), residues: 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1308 time to fit residues: 7.0784 Evaluate side-chains 40 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093888 restraints weight = 4430.169| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.10 r_work: 0.2953 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3316 Z= 0.233 Angle : 0.593 7.717 4520 Z= 0.289 Chirality : 0.039 0.120 528 Planarity : 0.003 0.023 546 Dihedral : 4.468 16.120 449 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.58 % 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: -0.79 (0.43), residues: 398 helix: -0.19 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.31 (0.73), residues: 83 =============================================================================== Job complete usr+sys time: 1078.71 seconds wall clock time: 20 minutes 3.22 seconds (1203.22 seconds total)