Starting phenix.real_space_refine on Sun Mar 10 17:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz4_15034/03_2024/7zz4_15034_updated.pdb" } resolution = 2.63 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 12 5.16 5 C 2305 2.51 5 N 643 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3682 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3682 Unusual residues: {' MG': 1, 'ACO': 1, 'ATP': 1} Classifications: {'peptide': 463, 'undetermined': 3, 'water': 11} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 443, None: 14} Not linked: pdbres="GLY A 461 " pdbres="ATP A1201 " Not linked: pdbres="ATP A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="ACO A1203 " Not linked: pdbres="ACO A1203 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " ... (remaining 9 not shown) Time building chain proxies: 2.40, per 1000 atoms: 0.65 Number of scatterers: 3682 At special positions: 0 Unit cell: (66.78, 74.2, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 6 15.00 Mg 1 11.99 O 715 8.00 N 643 7.00 C 2305 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: 1.57 Conformation dependent library (CDL) restraints added in 811.1 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 6 sheets defined 33.7% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 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 60 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 173 through 190 Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.413A pdb=" N THR A 296 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 297 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.756A 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 400 through 413 Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 433 through 436 No H-bonds generated for 'chain 'A' and resid 433 through 436' 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: 6.527A pdb=" N SER A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 6 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 28 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU A 46 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR A 31 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR A 48 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= C, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.867A pdb=" N GLU A 286 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 276 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE A 284 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 278 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 5.038A 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 230 through 232 removed outlier: 3.964A pdb=" N VAL A 230 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 238 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG A 232 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 15.376A pdb=" N GLN A 235 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N THR A 343 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 360 through 362 removed outlier: 4.179A pdb=" N THR A 360 " --> pdb=" O ARG A 417 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 384 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: 1.18 Time building geometry restraints manager: 1.64 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: 626 1.31 - 1.44: 951 1.44 - 1.56: 2136 1.56 - 1.69: 12 1.69 - 1.82: 18 Bond restraints: 3743 Sorted by residual: bond pdb=" C5A ACO A1203 " pdb=" N7A ACO A1203 " ideal model delta sigma weight residual 1.387 1.518 -0.131 1.00e-02 1.00e+04 1.72e+02 bond pdb=" C6A ACO A1203 " pdb=" N6A ACO A1203 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.28e+02 bond pdb=" C8A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 1.370 1.269 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C5P ACO A1203 " pdb=" N4P ACO A1203 " ideal model delta sigma weight residual 1.331 1.446 -0.115 1.20e-02 6.94e+03 9.22e+01 bond pdb=" C9P ACO A1203 " pdb=" N8P ACO A1203 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3738 not shown) Histogram of bond angle deviations from ideal: 98.21 - 106.51: 110 106.51 - 114.82: 2212 114.82 - 123.12: 2554 123.12 - 131.43: 197 131.43 - 139.74: 5 Bond angle restraints: 5078 Sorted by residual: angle pdb=" C4A ACO A1203 " pdb=" N9A ACO A1203 " pdb=" C8A ACO A1203 " ideal model delta sigma weight residual 105.72 122.41 -16.69 1.00e+00 1.00e+00 2.78e+02 angle pdb=" P1A ACO A1203 " pdb=" O3A ACO A1203 " pdb=" P2A ACO A1203 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.89e+02 angle pdb=" C ACO A1203 " pdb=" S1P ACO A1203 " pdb=" C2P ACO A1203 " ideal model delta sigma weight residual 101.25 112.32 -11.07 1.00e+00 1.00e+00 1.23e+02 angle pdb=" N3A ACO A1203 " pdb=" C4A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 127.04 137.63 -10.59 1.15e+00 7.59e-01 8.50e+01 angle pdb=" N7A ACO A1203 " pdb=" C8A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 114.08 105.24 8.84 1.00e+00 1.00e+00 7.81e+01 ... (remaining 5073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1908 16.98 - 33.96: 260 33.96 - 50.94: 79 50.94 - 67.92: 23 67.92 - 84.90: 9 Dihedral angle restraints: 2279 sinusoidal: 961 harmonic: 1318 Sorted by residual: dihedral pdb=" CA ASN A 288 " pdb=" CB ASN A 288 " pdb=" CG ASN A 288 " pdb=" OD1 ASN A 288 " ideal model delta sinusoidal sigma weight residual 120.00 -168.40 -71.60 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 46 " pdb=" CG GLU A 46 " pdb=" CD GLU A 46 " pdb=" OE1 GLU A 46 " ideal model delta sinusoidal sigma weight residual 0.00 84.90 -84.90 1 3.00e+01 1.11e-03 9.72e+00 dihedral pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " pdb=" CG GLU A 195 " pdb=" CD GLU A 195 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 418 0.047 - 0.093: 94 0.093 - 0.139: 41 0.139 - 0.186: 3 0.186 - 0.232: 3 Chirality restraints: 559 Sorted by residual: chirality pdb=" C3B ACO A1203 " pdb=" C2B ACO A1203 " pdb=" C4B ACO A1203 " pdb=" O3B ACO A1203 " both_signs ideal model delta sigma weight residual False -2.76 -2.53 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C2B ACO A1203 " pdb=" C1B ACO A1203 " pdb=" C3B ACO A1203 " pdb=" O2B ACO A1203 " both_signs ideal model delta sigma weight residual False -2.72 -2.49 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP A 280 " pdb=" N ASP A 280 " pdb=" C ASP A 280 " pdb=" CB ASP A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 556 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 349 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" CG ASN A 349 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 349 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 396 " -0.012 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 396 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 396 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 396 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 396 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 396 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 396 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 414 " -0.014 2.00e-02 2.50e+03 1.31e-02 3.01e+00 pdb=" CG PHE A 414 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 414 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 414 " -0.003 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 50 2.61 - 3.18: 3109 3.18 - 3.75: 6350 3.75 - 4.33: 8589 4.33 - 4.90: 13784 Nonbonded interactions: 31882 Sorted by model distance: nonbonded pdb=" O1G ATP A1201 " pdb="MG MG A1202 " model vdw 2.035 2.170 nonbonded pdb=" OE2 GLU A 286 " pdb="MG MG A1202 " model vdw 2.052 2.170 nonbonded pdb=" O3A ATP A1201 " pdb="MG MG A1202 " model vdw 2.068 2.170 nonbonded pdb=" O3B ATP A1201 " pdb="MG MG A1202 " model vdw 2.157 2.170 nonbonded pdb=" O1A ATP A1201 " pdb="MG MG A1202 " model vdw 2.174 2.170 ... (remaining 31877 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: 1.480 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: 5.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.090 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 0.131 3743 Z= 0.506 Angle : 1.052 16.688 5078 Z= 0.690 Chirality : 0.050 0.232 559 Planarity : 0.004 0.032 660 Dihedral : 18.143 84.903 1439 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.27 % Allowed : 21.22 % Favored : 78.51 % 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: -0.79 (0.37), residues: 461 helix: 0.24 (0.38), residues: 177 sheet: -0.52 (0.49), residues: 105 loop : -1.18 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 222 PHE 0.031 0.003 PHE A 396 TYR 0.012 0.002 TYR A 82 ARG 0.008 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.420 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 1.2827 time to fit residues: 26.9037 Evaluate side-chains 17 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS A 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3743 Z= 0.417 Angle : 0.637 6.506 5078 Z= 0.340 Chirality : 0.046 0.176 559 Planarity : 0.004 0.030 660 Dihedral : 12.670 86.933 592 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.33 % Allowed : 20.16 % Favored : 78.51 % 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: -0.18 (0.38), residues: 461 helix: 0.85 (0.39), residues: 179 sheet: -0.08 (0.49), residues: 104 loop : -1.07 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 222 PHE 0.014 0.002 PHE A 396 TYR 0.014 0.002 TYR A 82 ARG 0.003 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7397 (mtp85) outliers start: 5 outliers final: 2 residues processed: 21 average time/residue: 1.0535 time to fit residues: 23.4209 Evaluate side-chains 18 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3743 Z= 0.255 Angle : 0.521 5.825 5078 Z= 0.282 Chirality : 0.043 0.186 559 Planarity : 0.003 0.022 660 Dihedral : 12.153 87.708 592 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.86 % Allowed : 19.89 % Favored : 78.25 % 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: 0.26 (0.39), residues: 461 helix: 1.26 (0.39), residues: 178 sheet: 0.29 (0.52), residues: 97 loop : -0.93 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.009 0.002 PHE A 386 TYR 0.011 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) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7398 (mtp85) REVERT: A 226 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8538 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 26 average time/residue: 1.2079 time to fit residues: 32.8260 Evaluate side-chains 20 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 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 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.218 Angle : 0.525 7.723 5078 Z= 0.282 Chirality : 0.043 0.185 559 Planarity : 0.003 0.023 660 Dihedral : 11.857 86.026 592 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.59 % Allowed : 20.16 % Favored : 78.25 % 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: 0.41 (0.39), residues: 461 helix: 1.40 (0.39), residues: 178 sheet: 0.46 (0.52), residues: 97 loop : -0.91 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 177 PHE 0.013 0.001 PHE A 396 TYR 0.010 0.001 TYR A 82 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7365 (mtp85) REVERT: A 226 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8619 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 1.2220 time to fit residues: 28.2449 Evaluate side-chains 21 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.187 Angle : 0.483 4.859 5078 Z= 0.264 Chirality : 0.043 0.185 559 Planarity : 0.003 0.020 660 Dihedral : 11.588 84.724 592 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.92 % Allowed : 19.36 % Favored : 77.72 % 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: 0.57 (0.39), residues: 461 helix: 1.51 (0.40), residues: 178 sheet: 0.56 (0.53), residues: 97 loop : -0.81 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: A 226 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8686 (mtm-85) outliers start: 11 outliers final: 3 residues processed: 26 average time/residue: 1.4026 time to fit residues: 37.9863 Evaluate side-chains 20 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 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 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.202 Angle : 0.513 8.464 5078 Z= 0.273 Chirality : 0.043 0.184 559 Planarity : 0.003 0.022 660 Dihedral : 11.498 83.464 592 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 20.16 % Favored : 77.72 % 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: 0.63 (0.39), residues: 461 helix: 1.53 (0.40), residues: 178 sheet: 0.61 (0.53), residues: 97 loop : -0.76 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 177 PHE 0.025 0.002 PHE A 414 TYR 0.010 0.001 TYR A 82 ARG 0.001 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7149 (mtp85) REVERT: A 226 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8687 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 26 average time/residue: 1.1319 time to fit residues: 30.7989 Evaluate side-chains 21 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.161 Angle : 0.489 6.779 5078 Z= 0.260 Chirality : 0.043 0.185 559 Planarity : 0.003 0.024 660 Dihedral : 11.244 82.844 592 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.39 % Allowed : 20.69 % Favored : 76.92 % 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: 0.74 (0.39), residues: 461 helix: 1.59 (0.40), residues: 178 sheet: 0.81 (0.53), residues: 95 loop : -0.73 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.018 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 19 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8137 (ptp) REVERT: A 168 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: A 226 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8522 (mtm-85) REVERT: A 458 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7856 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 1.3445 time to fit residues: 35.0807 Evaluate side-chains 23 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 16 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.213 Angle : 0.534 8.929 5078 Z= 0.279 Chirality : 0.043 0.183 559 Planarity : 0.003 0.023 660 Dihedral : 11.265 80.735 592 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 21.22 % Favored : 76.66 % 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: 0.73 (0.39), residues: 461 helix: 1.57 (0.40), residues: 178 sheet: 0.68 (0.53), residues: 97 loop : -0.66 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 177 PHE 0.019 0.002 PHE A 414 TYR 0.010 0.001 TYR A 82 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7144 (mtp85) REVERT: A 226 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8697 (mtm-85) REVERT: A 458 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7866 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 23 average time/residue: 1.2102 time to fit residues: 29.2165 Evaluate side-chains 21 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 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 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.212 Angle : 0.510 5.939 5078 Z= 0.270 Chirality : 0.043 0.183 559 Planarity : 0.003 0.022 660 Dihedral : 11.240 80.055 592 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.92 % Allowed : 20.69 % Favored : 76.39 % 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: 0.73 (0.39), residues: 461 helix: 1.54 (0.40), residues: 178 sheet: 0.69 (0.52), residues: 97 loop : -0.63 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.019 0.002 PHE A 414 TYR 0.010 0.001 TYR A 82 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8212 (p0) REVERT: A 168 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7148 (mtp85) REVERT: A 226 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8698 (mtm-85) REVERT: A 458 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7877 (mtm-85) outliers start: 11 outliers final: 5 residues processed: 26 average time/residue: 1.3082 time to fit residues: 35.5042 Evaluate side-chains 24 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 3743 Z= 0.266 Angle : 1.167 59.200 5078 Z= 0.708 Chirality : 0.052 0.690 559 Planarity : 0.003 0.049 660 Dihedral : 11.284 80.052 592 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.39 % Allowed : 21.22 % Favored : 76.39 % Cbeta Deviations : 0.24 % 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: 0.74 (0.39), residues: 461 helix: 1.55 (0.40), residues: 178 sheet: 0.69 (0.52), residues: 97 loop : -0.62 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS A 177 PHE 0.017 0.001 PHE A 414 TYR 0.010 0.001 TYR A 82 ARG 0.004 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 16 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7151 (mtp85) REVERT: A 226 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8697 (mtm-85) REVERT: A 458 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7877 (mtm-85) outliers start: 9 outliers final: 5 residues processed: 23 average time/residue: 1.2602 time to fit residues: 30.3436 Evaluate side-chains 23 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 16 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 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 135 ASN ** 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 = 0.3475 r_free = 0.3475 target = 0.064344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057432 restraints weight = 14731.484| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.66 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 3743 Z= 0.266 Angle : 1.167 59.200 5078 Z= 0.708 Chirality : 0.052 0.690 559 Planarity : 0.003 0.049 660 Dihedral : 11.284 80.052 592 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.86 % Allowed : 21.75 % Favored : 76.39 % Cbeta Deviations : 0.24 % 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: 0.74 (0.39), residues: 461 helix: 1.55 (0.40), residues: 178 sheet: 0.69 (0.52), residues: 97 loop : -0.62 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS A 177 PHE 0.017 0.001 PHE A 414 TYR 0.010 0.001 TYR A 82 ARG 0.004 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.52 seconds wall clock time: 27 minutes 5.62 seconds (1625.62 seconds total)