Starting phenix.real_space_refine on Sun Mar 10 17:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/03_2024/7zz5_15035_updated.pdb" } resolution = 2.43 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= 0.008 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 12 5.16 5 C 2291 2.51 5 N 636 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" 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: 3633 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3633 Unusual residues: {'ACO': 1, 'BCT': 1} Classifications: {'peptide': 461, 'undetermined': 2} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 441, None: 2} Not linked: pdbres="ARG A 460 " pdbres="ACO A1201 " Not linked: pdbres="ACO A1201 " pdbres="BCT A1202 " Time building chain proxies: 2.39, per 1000 atoms: 0.66 Number of scatterers: 3633 At special positions: 0 Unit cell: (64.66, 73.14, 74.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 3 15.00 O 691 8.00 N 636 7.00 C 2291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 788.5 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 6 sheets defined 34.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.516A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 56 through 59 No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.780A pdb=" N HIS A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.310A pdb=" N THR A 296 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 297 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 302 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 449 through 452 Processing sheet with id= A, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.299A pdb=" N SER A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 6 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 28 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 46 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR A 31 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR A 48 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 154 through 156 Processing sheet with id= C, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.910A pdb=" N GLU A 286 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU A 276 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE A 284 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 278 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 212 through 214 Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'A' and resid 360 through 362 128 hydrogen bonds defined for protein. 351 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: 1.07 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.44: 936 1.44 - 1.57: 2118 1.57 - 1.69: 6 1.69 - 1.82: 18 Bond restraints: 3703 Sorted by residual: bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.78e+02 bond pdb=" C6A ACO A1201 " pdb=" N6A ACO A1201 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.29e+02 bond pdb=" C5P ACO A1201 " pdb=" N4P ACO A1201 " ideal model delta sigma weight residual 1.331 1.451 -0.120 1.20e-02 6.94e+03 9.98e+01 bond pdb=" C8A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 1.370 1.270 0.100 1.00e-02 1.00e+04 9.97e+01 bond pdb=" C9P ACO A1201 " pdb=" N8P ACO A1201 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3698 not shown) Histogram of bond angle deviations from ideal: 95.75 - 104.24: 60 104.24 - 112.72: 1948 112.72 - 121.20: 2025 121.20 - 129.68: 963 129.68 - 138.16: 20 Bond angle restraints: 5016 Sorted by residual: angle pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " pdb=" C8A ACO A1201 " ideal model delta sigma weight residual 105.72 122.31 -16.59 1.00e+00 1.00e+00 2.75e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 124.19 12.64 1.00e+00 1.00e+00 1.60e+02 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 95.76 16.24 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N3A ACO A1201 " pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 127.04 137.47 -10.43 1.15e+00 7.59e-01 8.26e+01 angle pdb=" C ACO A1201 " pdb=" S1P ACO A1201 " pdb=" C2P ACO A1201 " ideal model delta sigma weight residual 101.25 110.12 -8.87 1.00e+00 1.00e+00 7.87e+01 ... (remaining 5011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1926 17.67 - 35.33: 222 35.33 - 53.00: 60 53.00 - 70.67: 21 70.67 - 88.34: 11 Dihedral angle restraints: 2240 sinusoidal: 926 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU A 175 " pdb=" C GLU A 175 " pdb=" N MET A 176 " pdb=" CA MET A 176 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE A 131 " pdb=" C ILE A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 82 " pdb=" C TYR A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 429 0.057 - 0.113: 106 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 3 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3B ACO A1201 " pdb=" C2B ACO A1201 " pdb=" C4B ACO A1201 " pdb=" O3B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.76 -2.49 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2B ACO A1201 " pdb=" C1B ACO A1201 " pdb=" C3B ACO A1201 " pdb=" O2B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 551 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A1202 " 0.084 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" O1 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O2 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BCT A1202 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 131 " 0.083 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 132 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 459 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP A 459 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 460 " 0.015 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 820 2.78 - 3.31: 3384 3.31 - 3.84: 6604 3.84 - 4.37: 7615 4.37 - 4.90: 12740 Nonbonded interactions: 31163 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" OH TYR A 82 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 329 " pdb=" OE1 GLU A 330 " model vdw 2.332 2.440 nonbonded pdb=" OG1 THR A 296 " pdb=" OE1 GLN A 339 " model vdw 2.333 2.440 nonbonded pdb=" O LYS A 157 " pdb=" NZ LYS A 157 " model vdw 2.346 2.520 nonbonded pdb=" OE1 GLU A 46 " pdb=" OH TYR A 48 " model vdw 2.350 2.440 ... (remaining 31158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.340 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.520 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.008 0.173 3703 Z= 0.622 Angle : 1.042 17.316 5016 Z= 0.656 Chirality : 0.052 0.283 554 Planarity : 0.006 0.114 658 Dihedral : 17.808 88.336 1402 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.86 % Allowed : 16.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.36), residues: 459 helix: -0.40 (0.35), residues: 179 sheet: 0.39 (0.58), residues: 79 loop : -1.26 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 222 PHE 0.028 0.002 PHE A 367 TYR 0.011 0.001 TYR A 82 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.417 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.7512 time to fit residues: 19.4000 Evaluate side-chains 23 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN A 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3703 Z= 0.236 Angle : 0.470 6.651 5016 Z= 0.252 Chirality : 0.043 0.142 554 Planarity : 0.003 0.032 658 Dihedral : 10.750 82.681 565 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.66 % Allowed : 15.69 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.38), residues: 459 helix: 0.59 (0.38), residues: 179 sheet: 0.72 (0.60), residues: 77 loop : -1.04 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.015 0.001 PHE A 191 TYR 0.006 0.001 TYR A 361 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 0.469 Fit side-chains REVERT: A 155 MET cc_start: 0.7186 (tmm) cc_final: 0.6695 (tmm) REVERT: A 196 ILE cc_start: 0.4414 (OUTLIER) cc_final: 0.4018 (mp) REVERT: A 414 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8254 (t80) outliers start: 10 outliers final: 3 residues processed: 28 average time/residue: 0.8182 time to fit residues: 24.4004 Evaluate side-chains 23 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.0170 chunk 31 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3703 Z= 0.206 Angle : 0.467 7.837 5016 Z= 0.248 Chirality : 0.044 0.216 554 Planarity : 0.003 0.022 658 Dihedral : 9.640 83.849 560 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.66 % Allowed : 15.16 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.39), residues: 459 helix: 0.87 (0.39), residues: 185 sheet: 0.66 (0.60), residues: 78 loop : -1.00 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.014 0.001 PHE A 146 TYR 0.007 0.001 TYR A 82 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 22 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 132 PRO cc_start: 0.7431 (Cg_endo) cc_final: 0.7205 (Cg_exo) REVERT: A 155 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6592 (tmm) REVERT: A 196 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4615 (mp) REVERT: A 414 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8281 (t80) outliers start: 10 outliers final: 3 residues processed: 30 average time/residue: 0.8260 time to fit residues: 26.2802 Evaluate side-chains 24 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3703 Z= 0.209 Angle : 0.466 6.833 5016 Z= 0.248 Chirality : 0.043 0.152 554 Planarity : 0.003 0.023 658 Dihedral : 9.192 84.768 558 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.19 % Allowed : 15.16 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.39), residues: 459 helix: 1.00 (0.39), residues: 185 sheet: 0.76 (0.60), residues: 78 loop : -0.89 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.011 0.001 PHE A 146 TYR 0.011 0.001 TYR A 150 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 21 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6574 (tmm) REVERT: A 414 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8254 (t80) outliers start: 12 outliers final: 4 residues processed: 31 average time/residue: 1.0132 time to fit residues: 32.9933 Evaluate side-chains 26 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 224 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3703 Z= 0.273 Angle : 0.506 8.275 5016 Z= 0.267 Chirality : 0.044 0.141 554 Planarity : 0.004 0.052 658 Dihedral : 9.309 85.600 558 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 15.96 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.40), residues: 459 helix: 0.99 (0.39), residues: 187 sheet: 0.52 (0.57), residues: 88 loop : -0.83 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.009 0.002 PHE A 275 TYR 0.009 0.001 TYR A 150 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 23 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8336 (t80) outliers start: 10 outliers final: 5 residues processed: 31 average time/residue: 1.2095 time to fit residues: 39.1797 Evaluate side-chains 27 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 44 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3703 Z= 0.140 Angle : 0.472 9.039 5016 Z= 0.245 Chirality : 0.043 0.135 554 Planarity : 0.003 0.021 658 Dihedral : 9.023 86.145 558 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.66 % Allowed : 16.22 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.40), residues: 459 helix: 1.11 (0.40), residues: 185 sheet: 0.69 (0.58), residues: 87 loop : -0.93 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.008 0.001 PHE A 275 TYR 0.006 0.001 TYR A 150 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 23 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8991 (tp) REVERT: A 414 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8266 (t80) outliers start: 10 outliers final: 5 residues processed: 32 average time/residue: 1.1163 time to fit residues: 37.3578 Evaluate side-chains 29 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3703 Z= 0.245 Angle : 0.508 9.231 5016 Z= 0.265 Chirality : 0.044 0.134 554 Planarity : 0.003 0.044 658 Dihedral : 9.106 85.936 558 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.39 % Allowed : 17.29 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.40), residues: 459 helix: 1.08 (0.39), residues: 185 sheet: 0.53 (0.57), residues: 89 loop : -0.84 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.009 0.001 PHE A 275 TYR 0.007 0.001 TYR A 361 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8331 (t80) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.9786 time to fit residues: 31.9726 Evaluate side-chains 29 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3703 Z= 0.162 Angle : 0.481 9.514 5016 Z= 0.251 Chirality : 0.043 0.137 554 Planarity : 0.003 0.053 658 Dihedral : 8.937 86.209 558 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.66 % Allowed : 17.02 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.40), residues: 459 helix: 1.12 (0.40), residues: 185 sheet: 0.70 (0.58), residues: 87 loop : -0.89 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.008 0.001 PHE A 275 TYR 0.006 0.001 TYR A 82 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8988 (tp) REVERT: A 176 MET cc_start: 0.6357 (mmt) cc_final: 0.6042 (mpm) REVERT: A 414 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8270 (t80) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 1.0910 time to fit residues: 37.6532 Evaluate side-chains 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3703 Z= 0.201 Angle : 0.495 9.745 5016 Z= 0.257 Chirality : 0.043 0.134 554 Planarity : 0.003 0.049 658 Dihedral : 8.942 86.051 558 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 17.55 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.40), residues: 459 helix: 1.12 (0.39), residues: 185 sheet: 0.58 (0.58), residues: 89 loop : -0.82 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.015 0.001 PHE A 396 TYR 0.007 0.001 TYR A 180 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8282 (t80) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 1.0246 time to fit residues: 32.3511 Evaluate side-chains 30 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3703 Z= 0.185 Angle : 0.514 9.890 5016 Z= 0.264 Chirality : 0.044 0.153 554 Planarity : 0.003 0.051 658 Dihedral : 8.901 86.095 558 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.39 % Allowed : 17.82 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.40), residues: 459 helix: 1.11 (0.40), residues: 185 sheet: 0.61 (0.58), residues: 89 loop : -0.81 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.010 0.001 PHE A 367 TYR 0.010 0.001 TYR A 180 ARG 0.002 0.000 ARG A 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.6521 (mmt) cc_final: 0.6264 (mpm) REVERT: A 414 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8296 (t80) outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 1.0486 time to fit residues: 31.9880 Evaluate side-chains 30 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053862 restraints weight = 12145.380| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.16 r_work: 0.3040 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3703 Z= 0.201 Angle : 0.521 10.015 5016 Z= 0.266 Chirality : 0.044 0.133 554 Planarity : 0.003 0.020 658 Dihedral : 8.926 85.966 558 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 18.09 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.40), residues: 459 helix: 1.08 (0.39), residues: 185 sheet: 0.83 (0.60), residues: 79 loop : -0.78 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.010 0.001 PHE A 367 TYR 0.011 0.001 TYR A 180 ARG 0.002 0.000 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.82 seconds wall clock time: 29 minutes 30.04 seconds (1770.04 seconds total)