Starting phenix.real_space_refine on Fri Apr 5 13:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2024/7rtv_24690.pdb" } resolution = 3.96 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= 0.044 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 25 5.16 5 C 1846 2.51 5 N 460 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2881 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2803 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 7, 'TRANS': 358} Chain breaks: 1 Chain: "B" 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: "C" 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 Time building chain proxies: 2.10, per 1000 atoms: 0.73 Number of scatterers: 2881 At special positions: 0 Unit cell: (62.863, 52.669, 135.92, 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 25 16.00 O 550 8.00 N 460 7.00 C 1846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 129 " " NAG C 1 " - " ASN A 352 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 523.3 milliseconds 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 4.152A pdb=" N CYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 240 through 274 removed outlier: 3.951A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.318A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 removed outlier: 3.507A pdb=" N LEU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.618A pdb=" N GLU A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 409 removed outlier: 4.054A pdb=" N ASP A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 280 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.47 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: 903 1.34 - 1.46: 530 1.46 - 1.58: 1465 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2932 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.574 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C1 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 2927 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 40 106.20 - 113.14: 1678 113.14 - 120.08: 1051 120.08 - 127.02: 1198 127.02 - 133.97: 22 Bond angle restraints: 3989 Sorted by residual: angle pdb=" C GLN A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.58 113.37 8.21 1.95e+00 2.63e-01 1.77e+01 angle pdb=" CA MET A 177 " pdb=" CB MET A 177 " pdb=" CG MET A 177 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.33e+00 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 121.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" N MET A 177 " pdb=" CA MET A 177 " pdb=" CB MET A 177 " ideal model delta sigma weight residual 110.41 115.33 -4.92 1.68e+00 3.54e-01 8.59e+00 angle pdb=" CA GLN A 144 " pdb=" CB GLN A 144 " pdb=" CG GLN A 144 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.37e+00 ... (remaining 3984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 1630 24.21 - 48.42: 102 48.42 - 72.63: 32 72.63 - 96.84: 10 96.84 - 121.05: 30 Dihedral angle restraints: 1804 sinusoidal: 746 harmonic: 1058 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 172.83 -79.83 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 132.56 -39.56 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 167.66 121.05 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 1801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 412 0.054 - 0.107: 78 0.107 - 0.161: 7 0.161 - 0.214: 3 0.214 - 0.268: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 499 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 410 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 411 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ILE A 381 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 382 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C CYS A 382 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS A 382 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 383 " -0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 387 2.75 - 3.28: 3201 3.28 - 3.82: 5090 3.82 - 4.36: 5147 4.36 - 4.90: 8800 Nonbonded interactions: 22625 Sorted by model distance: nonbonded pdb=" O SER A 256 " pdb=" OG SER A 396 " model vdw 2.207 2.440 nonbonded pdb=" O GLY A 117 " pdb=" NE2 GLN A 120 " model vdw 2.228 2.520 nonbonded pdb=" O SER A 183 " pdb=" OG SER A 186 " model vdw 2.259 2.440 nonbonded pdb=" O CYS A 300 " pdb=" NH2 ARG A 368 " model vdw 2.308 2.520 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE2 GLU A 209 " model vdw 2.319 2.520 ... (remaining 22620 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 'B' 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: 0.220 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: 1.100 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 12.510 Find NCS groups from input model: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 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 : 0.004 0.055 2932 Z= 0.257 Angle : 0.763 8.808 3989 Z= 0.350 Chirality : 0.045 0.268 502 Planarity : 0.005 0.080 486 Dihedral : 24.992 121.052 1118 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.32 % Allowed : 1.95 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.44), residues: 362 helix: 2.84 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.76 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 257 HIS 0.003 0.001 HIS A 359 PHE 0.022 0.002 PHE A 220 TYR 0.015 0.001 TYR A 66 ARG 0.003 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.281 Fit side-chains REVERT: A 127 ASN cc_start: 0.7972 (m110) cc_final: 0.7152 (m-40) REVERT: A 132 PHE cc_start: 0.7293 (m-80) cc_final: 0.7026 (m-10) REVERT: A 177 MET cc_start: 0.7020 (pmm) cc_final: 0.6597 (pmm) REVERT: A 372 LYS cc_start: 0.8838 (tttp) cc_final: 0.8365 (tttm) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1251 time to fit residues: 14.4158 Evaluate side-chains 76 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.0570 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 152 GLN A 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2932 Z= 0.182 Angle : 0.742 7.831 3989 Z= 0.340 Chirality : 0.045 0.255 502 Planarity : 0.004 0.048 486 Dihedral : 24.647 110.641 511 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 12.34 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.43), residues: 362 helix: 2.90 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.93 (1.09), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 257 HIS 0.003 0.001 HIS A 153 PHE 0.019 0.002 PHE A 395 TYR 0.018 0.001 TYR A 296 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.312 Fit side-chains REVERT: A 127 ASN cc_start: 0.7683 (m110) cc_final: 0.6806 (m-40) REVERT: A 150 LEU cc_start: 0.7982 (mt) cc_final: 0.7761 (mt) REVERT: A 177 MET cc_start: 0.7135 (pmm) cc_final: 0.6528 (pmm) REVERT: A 196 THR cc_start: 0.8052 (p) cc_final: 0.7837 (p) REVERT: A 401 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8505 (mp) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.1041 time to fit residues: 12.1213 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2932 Z= 0.192 Angle : 0.759 10.248 3989 Z= 0.338 Chirality : 0.045 0.242 502 Planarity : 0.004 0.035 486 Dihedral : 21.826 112.661 511 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 16.88 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.43), residues: 362 helix: 2.81 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.12 (1.06), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 359 PHE 0.021 0.002 PHE A 315 TYR 0.012 0.001 TYR A 296 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.252 Fit side-chains REVERT: A 127 ASN cc_start: 0.7929 (m110) cc_final: 0.7329 (m-40) REVERT: A 177 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6666 (pmm) REVERT: A 392 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7614 (tt) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.1036 time to fit residues: 11.8730 Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2932 Z= 0.177 Angle : 0.792 10.200 3989 Z= 0.349 Chirality : 0.049 0.298 502 Planarity : 0.004 0.028 486 Dihedral : 19.786 112.852 511 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.55 % Allowed : 19.48 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.43), residues: 362 helix: 2.81 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.01 (1.08), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.012 0.002 PHE A 308 TYR 0.011 0.001 TYR A 296 ARG 0.013 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.226 Fit side-chains REVERT: A 127 ASN cc_start: 0.7642 (m110) cc_final: 0.7120 (m-40) REVERT: A 177 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6691 (pmm) REVERT: A 395 PHE cc_start: 0.8051 (t80) cc_final: 0.7588 (t80) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1199 time to fit residues: 14.2935 Evaluate side-chains 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS A 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2932 Z= 0.178 Angle : 0.805 10.687 3989 Z= 0.358 Chirality : 0.047 0.286 502 Planarity : 0.004 0.034 486 Dihedral : 17.738 112.243 511 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.22 % Allowed : 20.45 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.44), residues: 362 helix: 2.88 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -2.10 (1.07), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 257 HIS 0.003 0.001 HIS A 359 PHE 0.012 0.002 PHE A 308 TYR 0.010 0.001 TYR A 296 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7413 (m110) cc_final: 0.6865 (m-40) REVERT: A 177 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6696 (pmm) REVERT: A 192 ARG cc_start: 0.6366 (tmt-80) cc_final: 0.6123 (tmt-80) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.1037 time to fit residues: 12.1167 Evaluate side-chains 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2932 Z= 0.182 Angle : 0.839 12.294 3989 Z= 0.365 Chirality : 0.047 0.320 502 Planarity : 0.004 0.039 486 Dihedral : 15.417 108.979 511 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.19 % Allowed : 24.03 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.44), residues: 362 helix: 2.91 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -2.10 (1.07), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.014 0.002 PHE A 315 TYR 0.009 0.001 TYR A 296 ARG 0.005 0.001 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.304 Fit side-chains REVERT: A 127 ASN cc_start: 0.7429 (m110) cc_final: 0.6652 (m-40) REVERT: A 177 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6288 (pmm) REVERT: A 315 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 355 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6883 (mm-30) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.1164 time to fit residues: 14.0517 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.6429 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 2932 Z= 0.190 Angle : 0.879 11.764 3989 Z= 0.386 Chirality : 0.047 0.294 502 Planarity : 0.004 0.027 486 Dihedral : 14.649 106.574 511 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.87 % Allowed : 24.68 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.44), residues: 362 helix: 2.87 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -2.05 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 PHE 0.011 0.001 PHE A 315 TYR 0.009 0.001 TYR A 296 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7859 (t0) cc_final: 0.7596 (t0) REVERT: A 177 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6233 (pmm) REVERT: A 315 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7809 (t80) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.1006 time to fit residues: 12.1122 Evaluate side-chains 98 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2932 Z= 0.197 Angle : 0.890 13.745 3989 Z= 0.393 Chirality : 0.049 0.319 502 Planarity : 0.004 0.028 486 Dihedral : 13.607 102.848 511 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.55 % Allowed : 27.60 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.44), residues: 362 helix: 2.72 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.03 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.002 0.001 HIS A 153 PHE 0.027 0.002 PHE A 220 TYR 0.009 0.001 TYR A 296 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7719 (m-40) cc_final: 0.7170 (m-40) REVERT: A 177 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6260 (pmm) REVERT: A 315 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 355 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6479 (mm-30) REVERT: A 359 HIS cc_start: 0.7727 (m-70) cc_final: 0.7416 (m-70) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.0966 time to fit residues: 11.0383 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2932 Z= 0.185 Angle : 0.885 14.696 3989 Z= 0.389 Chirality : 0.046 0.291 502 Planarity : 0.004 0.027 486 Dihedral : 12.491 97.460 511 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.22 % Allowed : 27.60 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.44), residues: 362 helix: 2.75 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.01 (1.08), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.002 0.001 HIS A 153 PHE 0.023 0.001 PHE A 220 TYR 0.009 0.001 TYR A 296 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7754 (t0) cc_final: 0.7521 (t0) REVERT: A 177 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6243 (pmm) REVERT: A 237 ARG cc_start: 0.6117 (tpt170) cc_final: 0.5722 (tpm170) REVERT: A 315 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7687 (t80) REVERT: A 375 LEU cc_start: 0.8648 (tp) cc_final: 0.8400 (tp) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.1180 time to fit residues: 13.3006 Evaluate side-chains 95 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2932 Z= 0.190 Angle : 0.910 14.587 3989 Z= 0.405 Chirality : 0.047 0.300 502 Planarity : 0.004 0.033 486 Dihedral : 11.897 93.045 511 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.55 % Allowed : 27.27 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.44), residues: 362 helix: 2.67 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.78 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.004 0.001 HIS A 359 PHE 0.022 0.002 PHE A 220 TYR 0.011 0.001 TYR A 296 ARG 0.007 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7725 (t0) cc_final: 0.7476 (t0) REVERT: A 177 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6223 (pmm) REVERT: A 236 ARG cc_start: 0.5585 (tpp80) cc_final: 0.5293 (tpp-160) REVERT: A 283 ASN cc_start: 0.7274 (t0) cc_final: 0.7042 (t0) REVERT: A 315 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 366 ASP cc_start: 0.6348 (t70) cc_final: 0.6015 (m-30) REVERT: A 375 LEU cc_start: 0.8617 (tp) cc_final: 0.8407 (tp) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1255 time to fit residues: 13.5735 Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.231626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.195908 restraints weight = 4555.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.202953 restraints weight = 2756.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.207850 restraints weight = 1880.351| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2932 Z= 0.214 Angle : 0.916 14.274 3989 Z= 0.411 Chirality : 0.047 0.298 502 Planarity : 0.004 0.028 486 Dihedral : 10.975 85.072 511 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.87 % Allowed : 27.60 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.44), residues: 362 helix: 2.61 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.80 (1.08), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 PHE 0.021 0.002 PHE A 220 TYR 0.008 0.001 TYR A 296 ARG 0.006 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 921.66 seconds wall clock time: 17 minutes 13.87 seconds (1033.87 seconds total)