Starting phenix.real_space_refine on Sun Mar 10 16:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htt_35017/03_2024/8htt_35017_trim_updated.pdb" } resolution = 3.6 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= 0.010 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 17 5.16 5 C 2181 2.51 5 N 517 2.21 5 O 577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 217": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3184 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 11, 'TRANS': 377} Chain breaks: 2 Chain: "A" 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: "C" 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'GCO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.76 Number of scatterers: 3292 At special positions: 0 Unit cell: (56.883, 67.92, 121.407, 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 17 16.00 O 577 8.00 N 517 7.00 C 2181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 431 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 1 " - " ASN B 79 " " NAG C 1 " - " ASN B 62 " " NAG D 1 " - " ASN B 127 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 706.4 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 51.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 109 removed outlier: 5.082A pdb=" N GLU B 102 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 105 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 251 Processing helix chain 'B' and resid 257 through 286 removed outlier: 3.979A pdb=" N TRP B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 263 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 317 Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.833A pdb=" N LEU B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR B 340 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 362 through 392 Proline residue: B 366 - end of helix removed outlier: 3.565A pdb=" N ILE B 380 " --> pdb=" O TRP B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 426 removed outlier: 3.602A pdb=" N LEU B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 444 through 459 Processing sheet with id= A, first strand: chain 'B' and resid 41 through 44 Processing sheet with id= B, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.841A pdb=" N LEU B 59 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 180 " --> pdb=" O LEU B 59 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 486 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: 0.84 Time building geometry restraints manager: 1.60 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: 953 1.34 - 1.46: 919 1.46 - 1.58: 1477 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 3376 Sorted by residual: bond pdb=" C PRO B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.28e-02 6.10e+03 6.62e+01 bond pdb=" C CYS B 128 " pdb=" N SER B 129 " ideal model delta sigma weight residual 1.332 1.442 -0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" C LEU B 382 " pdb=" N THR B 383 " ideal model delta sigma weight residual 1.335 1.254 0.080 1.31e-02 5.83e+03 3.77e+01 bond pdb=" C SER B 129 " pdb=" N GLU B 130 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.31e-02 5.83e+03 3.11e+01 bond pdb=" C VAL B 101 " pdb=" N GLU B 102 " ideal model delta sigma weight residual 1.335 1.273 0.062 1.30e-02 5.92e+03 2.27e+01 ... (remaining 3371 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 105 107.43 - 114.07: 2005 114.07 - 120.71: 1388 120.71 - 127.35: 1035 127.35 - 133.99: 46 Bond angle restraints: 4579 Sorted by residual: angle pdb=" O VAL B 101 " pdb=" C VAL B 101 " pdb=" N GLU B 102 " ideal model delta sigma weight residual 121.87 128.99 -7.12 9.70e-01 1.06e+00 5.39e+01 angle pdb=" CA VAL B 101 " pdb=" C VAL B 101 " pdb=" N GLU B 102 " ideal model delta sigma weight residual 117.15 110.01 7.14 1.14e+00 7.69e-01 3.92e+01 angle pdb=" CA CYS B 128 " pdb=" C CYS B 128 " pdb=" N SER B 129 " ideal model delta sigma weight residual 118.22 112.42 5.80 1.03e+00 9.43e-01 3.17e+01 angle pdb=" C VAL B 101 " pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta sigma weight residual 120.38 113.57 6.81 1.37e+00 5.33e-01 2.47e+01 angle pdb=" C SER B 129 " pdb=" N GLU B 130 " pdb=" CA GLU B 130 " ideal model delta sigma weight residual 120.28 126.38 -6.10 1.34e+00 5.57e-01 2.07e+01 ... (remaining 4574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 1903 23.60 - 47.20: 115 47.20 - 70.81: 22 70.81 - 94.41: 18 94.41 - 118.01: 10 Dihedral angle restraints: 2068 sinusoidal: 925 harmonic: 1143 Sorted by residual: dihedral pdb=" CB CYS B 74 " pdb=" SG CYS B 74 " pdb=" SG CYS B 128 " pdb=" CB CYS B 128 " ideal model delta sinusoidal sigma weight residual -86.00 -19.51 -66.49 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" C3 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -55.55 62.46 -118.01 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" N2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -178.19 -61.08 -117.11 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 2065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 543 0.348 - 0.697: 0 0.697 - 1.045: 0 1.045 - 1.393: 0 1.393 - 1.741: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" C5 GCO B 901 " pdb=" C4 GCO B 901 " pdb=" C6 GCO B 901 " pdb=" O5 GCO B 901 " both_signs ideal model delta sigma weight residual False -2.35 -0.61 -1.74 2.00e-01 2.50e+01 7.58e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C4 GCO B 901 " pdb=" C3 GCO B 901 " pdb=" C5 GCO B 901 " pdb=" O4 GCO B 901 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 541 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 328 " -0.028 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C VAL B 328 " 0.096 2.00e-02 2.50e+03 pdb=" O VAL B 328 " -0.038 2.00e-02 2.50e+03 pdb=" N THR B 329 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 327 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLY B 327 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 327 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL B 328 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 127 " 0.024 2.00e-02 2.50e+03 2.23e-02 6.24e+00 pdb=" CG ASN B 127 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 127 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 127 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.024 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 303 2.74 - 3.28: 3417 3.28 - 3.82: 5254 3.82 - 4.36: 5488 4.36 - 4.90: 9790 Nonbonded interactions: 24252 Sorted by model distance: nonbonded pdb=" OG SER B 301 " pdb=" NH1 ARG B 305 " model vdw 2.197 2.520 nonbonded pdb=" O ASN B 465 " pdb=" NH1 ARG B 468 " model vdw 2.224 2.520 nonbonded pdb=" O3 NAG C 1 " pdb=" O5 NAG C 2 " model vdw 2.265 2.440 nonbonded pdb=" O GLN B 178 " pdb=" OH TYR B 182 " model vdw 2.281 2.440 nonbonded pdb=" NZ LYS B 425 " pdb=" OD2 ASP B 434 " model vdw 2.282 2.520 ... (remaining 24247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 6.590 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.109 3376 Z= 0.364 Angle : 0.690 8.420 4579 Z= 0.420 Chirality : 0.087 1.741 544 Planarity : 0.004 0.056 537 Dihedral : 19.581 118.012 1322 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % 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: 1.48 (0.47), residues: 383 helix: 2.60 (0.39), residues: 214 sheet: 1.74 (0.67), residues: 61 loop : -3.16 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 261 HIS 0.001 0.000 HIS B 331 PHE 0.007 0.001 PHE B 276 TYR 0.009 0.001 TYR B 237 ARG 0.001 0.000 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.7598 (tmm) cc_final: 0.7361 (tmm) REVERT: B 358 ASP cc_start: 0.7083 (t0) cc_final: 0.6528 (t70) REVERT: B 424 MET cc_start: 0.8329 (tpt) cc_final: 0.7558 (tpp) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1441 time to fit residues: 13.5344 Evaluate side-chains 52 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3376 Z= 0.243 Angle : 0.675 7.717 4579 Z= 0.319 Chirality : 0.043 0.184 544 Planarity : 0.004 0.045 537 Dihedral : 16.138 107.415 585 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.19 % Allowed : 10.72 % Favored : 86.09 % 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: 1.13 (0.46), residues: 383 helix: 2.26 (0.37), residues: 211 sheet: 1.63 (0.70), residues: 62 loop : -3.06 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.001 0.000 HIS B 403 PHE 0.018 0.002 PHE B 229 TYR 0.016 0.002 TYR B 340 ARG 0.005 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.341 Fit side-chains REVERT: B 227 MET cc_start: 0.7721 (tmm) cc_final: 0.7417 (tmm) REVERT: B 244 TRP cc_start: 0.9343 (t-100) cc_final: 0.8982 (t-100) REVERT: B 270 MET cc_start: 0.8281 (mmm) cc_final: 0.8009 (mmm) REVERT: B 358 ASP cc_start: 0.7111 (t0) cc_final: 0.6375 (t70) REVERT: B 424 MET cc_start: 0.8270 (tpt) cc_final: 0.7533 (tpp) REVERT: B 442 ASP cc_start: 0.8935 (m-30) cc_final: 0.8733 (m-30) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 0.1433 time to fit residues: 11.2098 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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: 0.8196 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3376 Z= 0.221 Angle : 0.618 7.315 4579 Z= 0.298 Chirality : 0.040 0.168 544 Planarity : 0.003 0.045 537 Dihedral : 13.258 103.905 584 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.48 % Allowed : 12.75 % Favored : 83.77 % 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: 1.12 (0.46), residues: 383 helix: 2.28 (0.37), residues: 209 sheet: 1.69 (0.70), residues: 62 loop : -3.09 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 376 HIS 0.001 0.000 HIS B 331 PHE 0.022 0.002 PHE B 276 TYR 0.011 0.001 TYR B 340 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.7768 (tmm) cc_final: 0.7430 (tmm) REVERT: B 244 TRP cc_start: 0.9333 (t-100) cc_final: 0.8915 (t-100) REVERT: B 254 ASP cc_start: 0.8651 (p0) cc_final: 0.8315 (p0) REVERT: B 358 ASP cc_start: 0.7123 (t0) cc_final: 0.6392 (t70) REVERT: B 424 MET cc_start: 0.8280 (tpt) cc_final: 0.7433 (tpp) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.1329 time to fit residues: 10.5260 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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: 0.8202 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3376 Z= 0.205 Angle : 0.598 7.240 4579 Z= 0.292 Chirality : 0.039 0.164 544 Planarity : 0.003 0.047 537 Dihedral : 11.634 101.248 584 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.77 % Allowed : 16.23 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.46), residues: 383 helix: 2.26 (0.38), residues: 209 sheet: 1.65 (0.71), residues: 62 loop : -2.97 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 376 HIS 0.001 0.000 HIS B 331 PHE 0.028 0.002 PHE B 132 TYR 0.009 0.001 TYR B 340 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 TRP cc_start: 0.9336 (t-100) cc_final: 0.8939 (t-100) REVERT: B 270 MET cc_start: 0.8204 (mmm) cc_final: 0.7907 (mmm) REVERT: B 323 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8458 (pttt) REVERT: B 424 MET cc_start: 0.8245 (tpt) cc_final: 0.7591 (tpp) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.1450 time to fit residues: 10.4886 Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3376 Z= 0.181 Angle : 0.580 7.592 4579 Z= 0.281 Chirality : 0.038 0.165 544 Planarity : 0.003 0.047 537 Dihedral : 10.756 98.841 584 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.64 % Allowed : 16.81 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.46), residues: 383 helix: 2.28 (0.38), residues: 209 sheet: 1.80 (0.72), residues: 61 loop : -3.08 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.001 0.000 HIS B 403 PHE 0.022 0.002 PHE B 276 TYR 0.009 0.001 TYR B 340 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 TRP cc_start: 0.9338 (t-100) cc_final: 0.8954 (t-100) REVERT: B 270 MET cc_start: 0.8334 (mmm) cc_final: 0.8054 (mmm) REVERT: B 323 LYS cc_start: 0.8753 (ptpt) cc_final: 0.8467 (pttt) REVERT: B 424 MET cc_start: 0.8156 (tpt) cc_final: 0.7510 (tpp) REVERT: B 435 TRP cc_start: 0.9130 (p-90) cc_final: 0.8744 (p-90) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1354 time to fit residues: 11.0875 Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3376 Z= 0.331 Angle : 0.640 7.197 4579 Z= 0.315 Chirality : 0.039 0.160 544 Planarity : 0.004 0.047 537 Dihedral : 10.684 98.617 584 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.93 % Allowed : 16.81 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.46), residues: 383 helix: 2.27 (0.38), residues: 209 sheet: 1.60 (0.72), residues: 61 loop : -3.13 (0.51), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 435 HIS 0.002 0.001 HIS B 331 PHE 0.040 0.002 PHE B 276 TYR 0.008 0.001 TYR B 216 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.8964 (p0) cc_final: 0.8751 (p0) REVERT: B 227 MET cc_start: 0.7785 (tmm) cc_final: 0.7416 (tmm) REVERT: B 323 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8443 (pttt) REVERT: B 353 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9039 (p) REVERT: B 358 ASP cc_start: 0.7312 (t0) cc_final: 0.6581 (t70) REVERT: B 424 MET cc_start: 0.8246 (tpt) cc_final: 0.7550 (tpp) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.1376 time to fit residues: 10.9594 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3376 Z= 0.187 Angle : 0.598 7.448 4579 Z= 0.289 Chirality : 0.039 0.168 544 Planarity : 0.003 0.048 537 Dihedral : 10.395 97.096 584 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.06 % Allowed : 18.84 % Favored : 77.10 % 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: 1.10 (0.46), residues: 383 helix: 2.27 (0.38), residues: 209 sheet: 1.70 (0.73), residues: 61 loop : -3.09 (0.51), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 435 HIS 0.001 0.000 HIS B 331 PHE 0.030 0.002 PHE B 276 TYR 0.020 0.001 TYR B 277 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 244 TRP cc_start: 0.9353 (t-100) cc_final: 0.8978 (t-100) REVERT: B 323 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8442 (pttt) REVERT: B 358 ASP cc_start: 0.7289 (t0) cc_final: 0.6565 (t70) REVERT: B 424 MET cc_start: 0.8211 (tpt) cc_final: 0.7522 (tpp) REVERT: B 428 ILE cc_start: 0.8336 (tp) cc_final: 0.7988 (tp) REVERT: B 435 TRP cc_start: 0.9151 (p-90) cc_final: 0.8843 (p-90) outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.1353 time to fit residues: 11.4801 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3376 Z= 0.191 Angle : 0.615 7.741 4579 Z= 0.291 Chirality : 0.038 0.170 544 Planarity : 0.003 0.048 537 Dihedral : 10.227 96.111 584 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.61 % Allowed : 21.74 % Favored : 75.65 % 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: 1.07 (0.46), residues: 383 helix: 2.24 (0.38), residues: 209 sheet: 1.77 (0.73), residues: 61 loop : -3.12 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 435 HIS 0.000 0.000 HIS B 187 PHE 0.021 0.001 PHE B 276 TYR 0.008 0.001 TYR B 277 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8002 (t) REVERT: B 70 ASP cc_start: 0.7626 (p0) cc_final: 0.7419 (p0) REVERT: B 244 TRP cc_start: 0.9348 (t-100) cc_final: 0.8971 (t-100) REVERT: B 270 MET cc_start: 0.8254 (mmm) cc_final: 0.8039 (mmm) REVERT: B 323 LYS cc_start: 0.8746 (ptpt) cc_final: 0.8459 (pttt) REVERT: B 358 ASP cc_start: 0.7277 (t0) cc_final: 0.6468 (t70) REVERT: B 424 MET cc_start: 0.8182 (tpt) cc_final: 0.7515 (tpp) REVERT: B 428 ILE cc_start: 0.8318 (tp) cc_final: 0.7970 (tp) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.1363 time to fit residues: 11.0368 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3376 Z= 0.228 Angle : 0.620 7.257 4579 Z= 0.301 Chirality : 0.039 0.169 544 Planarity : 0.003 0.047 537 Dihedral : 10.138 95.539 584 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.19 % Allowed : 20.87 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.46), residues: 383 helix: 2.20 (0.38), residues: 211 sheet: 1.69 (0.73), residues: 61 loop : -3.10 (0.51), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 435 HIS 0.001 0.000 HIS B 403 PHE 0.019 0.002 PHE B 276 TYR 0.007 0.001 TYR B 94 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8001 (t) REVERT: B 92 GLU cc_start: 0.9124 (pt0) cc_final: 0.8923 (pm20) REVERT: B 323 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8448 (pttt) REVERT: B 358 ASP cc_start: 0.7206 (t0) cc_final: 0.6496 (t70) REVERT: B 424 MET cc_start: 0.8182 (tpt) cc_final: 0.7512 (tpp) REVERT: B 428 ILE cc_start: 0.8314 (tp) cc_final: 0.7955 (tp) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.1325 time to fit residues: 10.1871 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3376 Z= 0.209 Angle : 0.619 7.071 4579 Z= 0.301 Chirality : 0.039 0.172 544 Planarity : 0.003 0.048 537 Dihedral : 10.001 94.508 584 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.61 % Allowed : 22.03 % Favored : 75.36 % 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: 1.09 (0.47), residues: 383 helix: 2.21 (0.38), residues: 211 sheet: 1.80 (0.73), residues: 61 loop : -3.14 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 261 HIS 0.001 0.000 HIS B 403 PHE 0.017 0.002 PHE B 276 TYR 0.007 0.001 TYR B 340 ARG 0.002 0.000 ARG B 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.7991 (t) REVERT: B 70 ASP cc_start: 0.7641 (p0) cc_final: 0.7406 (p0) REVERT: B 323 LYS cc_start: 0.8749 (ptpt) cc_final: 0.8444 (pttt) REVERT: B 358 ASP cc_start: 0.7198 (t0) cc_final: 0.6460 (t70) REVERT: B 424 MET cc_start: 0.8234 (tpt) cc_final: 0.7372 (tpp) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1359 time to fit residues: 10.7482 Evaluate side-chains 66 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 434 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.088800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068851 restraints weight = 8102.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071409 restraints weight = 4067.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073166 restraints weight = 2705.124| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3376 Z= 0.211 Angle : 0.622 7.241 4579 Z= 0.305 Chirality : 0.039 0.172 544 Planarity : 0.003 0.048 537 Dihedral : 9.908 93.746 584 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.19 % Allowed : 21.45 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.46), residues: 383 helix: 2.19 (0.38), residues: 211 sheet: 1.74 (0.73), residues: 61 loop : -3.13 (0.51), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 435 HIS 0.001 0.000 HIS B 403 PHE 0.015 0.001 PHE B 276 TYR 0.008 0.001 TYR B 94 ARG 0.002 0.000 ARG B 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1057.79 seconds wall clock time: 19 minutes 38.54 seconds (1178.54 seconds total)