Starting phenix.real_space_refine on Mon Jun 24 17:04:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsn_32761/06_2024/7wsn_32761_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.116 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 14 5.16 5 C 2353 2.51 5 N 579 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3504 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'5RH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.84 Number of scatterers: 3567 At special positions: 0 Unit cell: (92.0125, 58.455, 72.5275, 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 14 16.00 O 621 8.00 N 579 7.00 C 2353 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 57 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 695.0 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 Processing helix chain 'A' and resid 48 through 62 removed outlier: 4.339A pdb=" N GLU A 53 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.705A pdb=" N VAL A 85 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 129 through 132 No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 136 through 163 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 167 through 191 removed outlier: 4.137A pdb=" N GLY A 170 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 172 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 Proline residue: A 212 - end of helix removed outlier: 3.631A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 303 through 317 removed outlier: 6.833A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 4.540A pdb=" N GLU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARG A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 372 Processing helix chain 'A' and resid 378 through 397 removed outlier: 4.054A pdb=" N TYR A 382 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 397 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 416 through 445 removed outlier: 5.161A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.504A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 255 hydrogen bonds defined for protein. 630 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: 0.91 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 542 1.31 - 1.43: 967 1.43 - 1.56: 2114 1.56 - 1.68: 1 1.68 - 1.81: 25 Bond restraints: 3649 Sorted by residual: bond pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 1.335 1.283 0.052 1.36e-02 5.41e+03 1.48e+01 bond pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.59e-02 3.96e+03 6.18e+00 bond pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N ASP A 252 " pdb=" CA ASP A 252 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.70e+00 ... (remaining 3644 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 93 106.04 - 113.04: 1991 113.04 - 120.04: 1450 120.04 - 127.03: 1396 127.03 - 134.03: 45 Bond angle restraints: 4975 Sorted by residual: angle pdb=" N ASN A 46 " pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 110.16 103.10 7.06 1.48e+00 4.57e-01 2.27e+01 angle pdb=" CA ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 118.48 122.63 -4.15 1.01e+00 9.80e-01 1.69e+01 angle pdb=" O ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 122.12 117.65 4.47 1.16e+00 7.43e-01 1.49e+01 angle pdb=" CA ASN A 46 " pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 120.42 116.59 3.83 1.06e+00 8.90e-01 1.31e+01 angle pdb=" CA SER A 412 " pdb=" C SER A 412 " pdb=" O SER A 412 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.29e+01 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 2137 35.67 - 71.33: 58 71.33 - 107.00: 3 107.00 - 142.67: 0 142.67 - 178.33: 2 Dihedral angle restraints: 2200 sinusoidal: 897 harmonic: 1303 Sorted by residual: dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O3 5RH A 601 " ideal model delta sinusoidal sigma weight residual 193.05 14.72 178.33 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O2 5RH A 601 " ideal model delta sinusoidal sigma weight residual 11.42 -165.41 176.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 381 0.038 - 0.075: 169 0.075 - 0.113: 44 0.113 - 0.150: 8 0.150 - 0.188: 1 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.24e+00 chirality pdb=" CG LEU A 206 " pdb=" CB LEU A 206 " pdb=" CD1 LEU A 206 " pdb=" CD2 LEU A 206 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PHE A 336 " pdb=" N PHE A 336 " pdb=" C PHE A 336 " pdb=" CB PHE A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 600 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " 0.062 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 57 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.027 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C18 5RH A 601 " 0.064 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.063 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.066 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C15 5RH A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.021 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.053 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.039 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 872 2.78 - 3.31: 3873 3.31 - 3.84: 5893 3.84 - 4.37: 6677 4.37 - 4.90: 11321 Nonbonded interactions: 28636 Sorted by model distance: nonbonded pdb=" OG SER A 89 " pdb=" ND2 ASN A 431 " model vdw 2.248 2.520 nonbonded pdb=" O GLY A 100 " pdb=" OG SER A 103 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR A 79 " pdb=" OH TYR A 440 " model vdw 2.261 2.440 nonbonded pdb=" O GLY A 92 " pdb=" OG SER A 95 " model vdw 2.372 2.440 nonbonded pdb=" NH2 ARG A 350 " pdb=" O PHE A 465 " model vdw 2.375 2.520 ... (remaining 28631 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: 0.530 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: 1.630 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.250 Find NCS groups from input model: 0.100 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: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.007 0.052 3649 Z= 0.476 Angle : 0.827 9.162 4975 Z= 0.458 Chirality : 0.044 0.188 603 Planarity : 0.006 0.049 616 Dihedral : 17.546 178.332 1372 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.08 % Allowed : 0.27 % Favored : 98.65 % 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: -0.44 (0.39), residues: 461 helix: 0.35 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -2.88 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 202 HIS 0.004 0.001 HIS A 353 PHE 0.014 0.002 PHE A 391 TYR 0.015 0.002 TYR A 148 ARG 0.009 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.386 Fit side-chains REVERT: A 264 LYS cc_start: 0.6249 (ttpt) cc_final: 0.5560 (pttm) REVERT: A 412 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (t) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1513 time to fit residues: 11.4663 Evaluate side-chains 45 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.0010 chunk 41 optimal weight: 0.7980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 413 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3649 Z= 0.237 Angle : 0.713 11.542 4975 Z= 0.346 Chirality : 0.043 0.188 603 Planarity : 0.006 0.051 616 Dihedral : 13.035 173.407 605 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.89 % Allowed : 14.05 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.41), residues: 461 helix: 1.25 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -2.91 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.019 0.002 PHE A 336 TYR 0.021 0.002 TYR A 148 ARG 0.003 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.371 Fit side-chains REVERT: A 264 LYS cc_start: 0.6232 (ttpt) cc_final: 0.5617 (pttm) REVERT: A 431 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8240 (t0) REVERT: A 434 ILE cc_start: 0.7551 (tp) cc_final: 0.7322 (tp) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1078 time to fit residues: 8.6071 Evaluate side-chains 53 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 299 GLN A 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3649 Z= 0.212 Angle : 0.637 10.361 4975 Z= 0.312 Chirality : 0.041 0.167 603 Planarity : 0.006 0.052 616 Dihedral : 12.479 164.783 604 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.70 % Allowed : 16.22 % Favored : 81.08 % 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: 1.00 (0.41), residues: 461 helix: 1.49 (0.29), residues: 370 sheet: None (None), residues: 0 loop : -2.89 (0.56), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 PHE 0.016 0.002 PHE A 336 TYR 0.015 0.001 TYR A 148 ARG 0.002 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.408 Fit side-chains REVERT: A 264 LYS cc_start: 0.6308 (ttpt) cc_final: 0.5736 (pttm) REVERT: A 346 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7089 (tmt170) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1169 time to fit residues: 8.8838 Evaluate side-chains 55 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 346 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3649 Z= 0.418 Angle : 0.732 9.165 4975 Z= 0.362 Chirality : 0.045 0.183 603 Planarity : 0.006 0.065 616 Dihedral : 12.778 166.704 602 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.51 % Allowed : 20.54 % Favored : 75.95 % 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: 0.73 (0.41), residues: 461 helix: 1.28 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.88 (0.58), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 404 HIS 0.001 0.001 HIS A 353 PHE 0.017 0.002 PHE A 336 TYR 0.010 0.002 TYR A 148 ARG 0.003 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.387 Fit side-chains REVERT: A 264 LYS cc_start: 0.6288 (ttpt) cc_final: 0.5998 (pttt) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.1110 time to fit residues: 8.1687 Evaluate side-chains 56 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 369 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.0470 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3649 Z= 0.177 Angle : 0.594 7.239 4975 Z= 0.295 Chirality : 0.039 0.137 603 Planarity : 0.006 0.052 616 Dihedral : 11.597 152.189 602 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 22.97 % Favored : 75.41 % 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: 1.26 (0.41), residues: 461 helix: 1.70 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -2.63 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.000 0.000 HIS A 284 PHE 0.015 0.001 PHE A 336 TYR 0.011 0.001 TYR A 229 ARG 0.003 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.314 Fit side-chains REVERT: A 264 LYS cc_start: 0.6213 (ttpt) cc_final: 0.5927 (pttt) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.1380 time to fit residues: 10.3784 Evaluate side-chains 58 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7372 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3649 Z= 0.201 Angle : 0.582 6.449 4975 Z= 0.291 Chirality : 0.039 0.124 603 Planarity : 0.006 0.054 616 Dihedral : 10.739 135.824 602 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 24.05 % Favored : 73.51 % 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: 1.34 (0.41), residues: 461 helix: 1.71 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.48 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.001 PHE A 336 TYR 0.011 0.001 TYR A 148 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.366 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.1134 time to fit residues: 8.2772 Evaluate side-chains 57 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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: 0.7375 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3649 Z= 0.216 Angle : 0.573 6.066 4975 Z= 0.289 Chirality : 0.039 0.123 603 Planarity : 0.006 0.058 616 Dihedral : 9.531 115.089 602 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 24.86 % Favored : 72.70 % 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: 1.33 (0.41), residues: 461 helix: 1.70 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.46 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 PHE 0.014 0.001 PHE A 336 TYR 0.011 0.001 TYR A 40 ARG 0.002 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.384 Fit side-chains REVERT: A 264 LYS cc_start: 0.6115 (ttpt) cc_final: 0.5819 (pttt) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.1224 time to fit residues: 8.8329 Evaluate side-chains 57 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 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: 0.7378 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3649 Z= 0.210 Angle : 0.560 6.084 4975 Z= 0.284 Chirality : 0.038 0.123 603 Planarity : 0.006 0.056 616 Dihedral : 9.052 110.773 602 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.43 % Allowed : 25.14 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.41), residues: 461 helix: 1.70 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.44 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.001 0.000 HIS A 167 PHE 0.015 0.001 PHE A 336 TYR 0.014 0.001 TYR A 229 ARG 0.001 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.371 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1280 time to fit residues: 9.2353 Evaluate side-chains 56 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7355 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3649 Z= 0.193 Angle : 0.549 6.055 4975 Z= 0.278 Chirality : 0.038 0.124 603 Planarity : 0.005 0.055 616 Dihedral : 8.973 110.272 602 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.89 % Allowed : 26.22 % Favored : 71.89 % 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: 1.37 (0.41), residues: 461 helix: 1.72 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.41 (0.55), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 PHE 0.014 0.001 PHE A 336 TYR 0.012 0.001 TYR A 229 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.396 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.1222 time to fit residues: 8.8925 Evaluate side-chains 55 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 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: 0.7343 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3649 Z= 0.189 Angle : 0.569 11.597 4975 Z= 0.282 Chirality : 0.038 0.124 603 Planarity : 0.006 0.053 616 Dihedral : 8.907 109.406 602 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.89 % Allowed : 27.03 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.41), residues: 461 helix: 1.74 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.37 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 PHE 0.014 0.001 PHE A 336 TYR 0.013 0.001 TYR A 229 ARG 0.001 0.000 ARG A 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.374 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.1217 time to fit residues: 8.8600 Evaluate side-chains 56 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.147300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114236 restraints weight = 4267.691| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.13 r_work: 0.3199 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3649 Z= 0.213 Angle : 0.580 11.191 4975 Z= 0.286 Chirality : 0.039 0.161 603 Planarity : 0.006 0.058 616 Dihedral : 8.912 109.865 602 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.62 % Allowed : 26.49 % Favored : 71.89 % 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: 1.44 (0.41), residues: 461 helix: 1.70 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.27 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 167 PHE 0.014 0.001 PHE A 336 TYR 0.012 0.001 TYR A 229 ARG 0.001 0.000 ARG A 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1172.98 seconds wall clock time: 21 minutes 53.89 seconds (1313.89 seconds total)