Starting phenix.real_space_refine on Mon Sep 23 13:52:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/09_2024/7xpz_33386.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/09_2024/7xpz_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_33386/09_2024/7xpz_33386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/09_2024/7xpz_33386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/09_2024/7xpz_33386.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpz_33386/09_2024/7xpz_33386.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.95, per 1000 atoms: 0.91 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 391.0 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: 0.31 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: 0.82 Time building geometry restraints manager: 0.81 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: 0.00 - 1.40: 4266 1.40 - 2.79: 206 2.79 - 4.19: 31 4.19 - 5.58: 12 5.58 - 6.98: 5 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 3.040 nonbonded pdb=" O THR A 404 " pdb=" OG1 THR A 408 " model vdw 2.319 3.040 nonbonded pdb=" OD2 ASP A 56 " pdb=" OG SER A 183 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.334 3.040 nonbonded pdb=" OG SER A 271 " pdb=" OD1 ASN A 403 " model vdw 2.337 3.040 ... (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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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 % Allowed : 9.51 % Favored : 89.91 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 274 HIS 0.001 0.000 HIS A 358 PHE 0.009 0.001 PHE A 276 TYR 0.010 0.002 TYR A 92 ARG 0.002 0.000 ARG A 264 *********************** 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 : 0.322 Fit side-chains REVERT: A 22 LEU cc_start: 0.6860 (tp) cc_final: 0.6364 (pp) REVERT: A 26 ARG cc_start: 0.6911 (tpt-90) cc_final: 0.6414 (ttm170) REVERT: A 40 GLN cc_start: 0.7794 (mm110) cc_final: 0.7521 (mm-40) REVERT: A 92 TYR cc_start: 0.8170 (m-80) cc_final: 0.7871 (m-80) REVERT: A 122 MET cc_start: 0.8952 (tmm) cc_final: 0.8715 (tmm) REVERT: A 310 ASP cc_start: 0.7621 (t0) cc_final: 0.7286 (t0) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.1875 time to fit residues: 12.7093 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 377 GLN A 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1863 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= 0.168 Angle : 0.544 5.654 4520 Z= 0.290 Chirality : 0.037 0.113 528 Planarity : 0.006 0.046 546 Dihedral : 5.431 34.845 451 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.02 % Allowed : 11.82 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.32), residues: 398 helix: -2.93 (0.21), residues: 310 sheet: None (None), residues: 0 loop : -2.34 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.009 0.001 PHE A 447 TYR 0.010 0.001 TYR A 35 ARG 0.007 0.000 ARG A 263 *********************** 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 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.406 Fit side-chains REVERT: A 22 LEU cc_start: 0.6895 (tp) cc_final: 0.6359 (pp) REVERT: A 26 ARG cc_start: 0.6986 (tpt-90) cc_final: 0.6491 (ttm170) REVERT: A 38 MET cc_start: 0.8523 (mmt) cc_final: 0.8286 (tpp) REVERT: A 122 MET cc_start: 0.9102 (tmm) cc_final: 0.8828 (tmm) REVERT: A 277 ASN cc_start: 0.8965 (t0) cc_final: 0.8574 (t0) REVERT: A 434 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7972 (tt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1785 time to fit residues: 10.8926 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3316 Z= 0.183 Angle : 0.531 5.960 4520 Z= 0.273 Chirality : 0.037 0.118 528 Planarity : 0.004 0.033 546 Dihedral : 4.751 18.878 449 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.73 % Allowed : 15.27 % Favored : 83.00 % 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: -3.12 (0.37), residues: 398 helix: -1.85 (0.25), residues: 313 sheet: None (None), residues: 0 loop : -2.05 (0.63), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.006 0.001 PHE A 165 TYR 0.011 0.001 TYR A 35 ARG 0.004 0.000 ARG A 263 *********************** 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 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.349 Fit side-chains REVERT: A 26 ARG cc_start: 0.6990 (tpt-90) cc_final: 0.6500 (ttm170) REVERT: A 122 MET cc_start: 0.8997 (tmm) cc_final: 0.8783 (ttp) REVERT: A 155 TYR cc_start: 0.7463 (m-10) cc_final: 0.7261 (m-10) REVERT: A 277 ASN cc_start: 0.8958 (t0) cc_final: 0.8607 (t0) REVERT: A 434 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7882 (tt) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.1429 time to fit residues: 8.5516 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU 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: 1.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3316 Z= 0.253 Angle : 0.551 6.060 4520 Z= 0.279 Chirality : 0.039 0.123 528 Planarity : 0.003 0.028 546 Dihedral : 4.738 17.950 449 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.73 % Allowed : 16.14 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.39), residues: 398 helix: -1.33 (0.27), residues: 313 sheet: None (None), residues: 0 loop : -1.78 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.017 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.003 0.000 ARG A 263 *********************** 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 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.347 Fit side-chains REVERT: A 26 ARG cc_start: 0.7029 (tpt-90) cc_final: 0.6493 (ttm170) REVERT: A 122 MET cc_start: 0.9006 (tmm) cc_final: 0.8799 (ttp) REVERT: A 155 TYR cc_start: 0.7476 (m-10) cc_final: 0.7220 (m-10) REVERT: A 277 ASN cc_start: 0.8933 (t0) cc_final: 0.8526 (t0) REVERT: A 357 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7967 (mpt-90) REVERT: A 434 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7811 (tt) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1683 time to fit residues: 9.9451 Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU 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: 0.9980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7605 moved from start: 0.2529 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= 0.252 Angle : 0.553 6.026 4520 Z= 0.279 Chirality : 0.039 0.124 528 Planarity : 0.003 0.026 546 Dihedral : 4.692 18.121 449 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.17 % Allowed : 15.27 % Favored : 81.56 % 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: -1.97 (0.41), residues: 398 helix: -1.04 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.63 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 273 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 276 TYR 0.011 0.001 TYR A 35 ARG 0.002 0.000 ARG A 263 *********************** 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 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7022 (tpt-90) cc_final: 0.6469 (ttm170) REVERT: A 155 TYR cc_start: 0.7458 (m-10) cc_final: 0.7167 (m-10) REVERT: A 277 ASN cc_start: 0.8960 (t0) cc_final: 0.8553 (t0) REVERT: A 357 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7901 (mpt-90) REVERT: A 413 ILE cc_start: 0.8204 (mm) cc_final: 0.7928 (mt) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1435 time to fit residues: 9.6960 Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.0070 chunk 12 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.180 Angle : 0.517 6.043 4520 Z= 0.261 Chirality : 0.038 0.117 528 Planarity : 0.003 0.025 546 Dihedral : 4.545 19.827 449 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.42), residues: 398 helix: -0.75 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.72 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 363 HIS 0.001 0.000 HIS A 358 PHE 0.020 0.001 PHE A 84 TYR 0.009 0.001 TYR A 92 ARG 0.002 0.000 ARG A 263 *********************** 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 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7013 (tpt-90) cc_final: 0.6462 (ttm170) REVERT: A 155 TYR cc_start: 0.7404 (m-10) cc_final: 0.7071 (m-10) REVERT: A 211 PHE cc_start: 0.8243 (m-80) cc_final: 0.7956 (m-80) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1447 time to fit residues: 9.4664 Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.210 Angle : 0.533 6.057 4520 Z= 0.269 Chirality : 0.039 0.118 528 Planarity : 0.003 0.025 546 Dihedral : 4.502 20.341 449 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.42), residues: 398 helix: -0.60 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.62 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.001 0.000 HIS A 114 PHE 0.014 0.001 PHE A 447 TYR 0.010 0.001 TYR A 92 ARG 0.002 0.000 ARG A 373 *********************** 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 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.347 Fit side-chains REVERT: A 26 ARG cc_start: 0.7037 (tpt-90) cc_final: 0.6484 (ttm170) REVERT: A 155 TYR cc_start: 0.7412 (m-10) cc_final: 0.7061 (m-10) REVERT: A 211 PHE cc_start: 0.8244 (m-80) cc_final: 0.7936 (m-80) REVERT: A 254 MET cc_start: 0.5880 (mtt) cc_final: 0.5528 (mtp) REVERT: A 357 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7869 (mpt-90) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.1638 time to fit residues: 10.3341 Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.2962 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= 0.197 Angle : 0.545 6.194 4520 Z= 0.274 Chirality : 0.038 0.124 528 Planarity : 0.003 0.025 546 Dihedral : 4.464 20.185 449 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.31 % Allowed : 16.71 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.43), residues: 398 helix: -0.46 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.49 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.000 0.000 HIS A 358 PHE 0.022 0.001 PHE A 84 TYR 0.010 0.001 TYR A 92 ARG 0.001 0.000 ARG A 263 *********************** 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 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.355 Fit side-chains REVERT: A 26 ARG cc_start: 0.7035 (tpt-90) cc_final: 0.6473 (ttm170) REVERT: A 155 TYR cc_start: 0.7349 (m-10) cc_final: 0.6994 (m-10) REVERT: A 211 PHE cc_start: 0.8217 (m-80) cc_final: 0.7757 (m-80) outliers start: 8 outliers final: 8 residues processed: 48 average time/residue: 0.1397 time to fit residues: 8.5457 Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.3029 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= 0.201 Angle : 0.550 6.264 4520 Z= 0.274 Chirality : 0.039 0.131 528 Planarity : 0.003 0.025 546 Dihedral : 4.421 20.002 449 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.43), residues: 398 helix: -0.42 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.54 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.000 0.000 HIS A 358 PHE 0.016 0.001 PHE A 447 TYR 0.011 0.001 TYR A 92 ARG 0.001 0.000 ARG A 263 *********************** 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 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.342 Fit side-chains REVERT: A 26 ARG cc_start: 0.7081 (tpt-90) cc_final: 0.6507 (ttm170) REVERT: A 155 TYR cc_start: 0.7308 (m-10) cc_final: 0.6935 (m-10) REVERT: A 211 PHE cc_start: 0.8215 (m-80) cc_final: 0.7865 (m-80) REVERT: A 357 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7904 (mpt-90) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.1597 time to fit residues: 9.6792 Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.3086 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= 0.184 Angle : 0.536 6.147 4520 Z= 0.266 Chirality : 0.038 0.125 528 Planarity : 0.003 0.025 546 Dihedral : 4.370 19.393 449 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.88 % Allowed : 16.14 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.43), residues: 398 helix: -0.30 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.55 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.000 0.000 HIS A 355 PHE 0.024 0.001 PHE A 84 TYR 0.010 0.001 TYR A 92 ARG 0.001 0.000 ARG A 263 ********************** 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 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.310 Fit side-chains REVERT: A 26 ARG cc_start: 0.7099 (tpt-90) cc_final: 0.6532 (ttm170) REVERT: A 155 TYR cc_start: 0.7290 (m-10) cc_final: 0.6913 (m-10) REVERT: A 211 PHE cc_start: 0.8201 (m-80) cc_final: 0.7785 (m-80) REVERT: A 357 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7877 (mpt-90) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1530 time to fit residues: 9.7043 Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 TRP Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098968 restraints weight = 4327.618| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.93 r_work: 0.3021 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.203 Angle : 0.565 8.018 4520 Z= 0.278 Chirality : 0.039 0.131 528 Planarity : 0.003 0.025 546 Dihedral : 4.385 19.381 449 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.31 % Allowed : 17.58 % Favored : 80.12 % 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 (0.42), residues: 398 helix: -0.28 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.55 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.000 0.000 HIS A 358 PHE 0.019 0.001 PHE A 447 TYR 0.010 0.001 TYR A 92 ARG 0.001 0.000 ARG A 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1095.69 seconds wall clock time: 20 minutes 15.38 seconds (1215.38 seconds total)