Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 01:27:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/04_2023/7zz5_15035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/04_2023/7zz5_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_15035/04_2023/7zz5_15035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/04_2023/7zz5_15035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/04_2023/7zz5_15035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz5_15035/04_2023/7zz5_15035_updated.pdb" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 2.46, per 1000 atoms: 0.68 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: 1.53 Conformation dependent library (CDL) restraints added in 636.5 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: 0.45 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: 1.05 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: 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: 1903 17.67 - 35.33: 210 35.33 - 53.00: 59 53.00 - 70.67: 17 70.67 - 88.34: 10 Dihedral angle restraints: 2199 sinusoidal: 885 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 2196 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: 1.130 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: 5.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- 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 : 17.330 88.336 1361 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 % 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 *********************** 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 : 0.374 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.7424 time to fit residues: 19.1359 Evaluate side-chains 23 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 3703 Z= 0.238 Angle : 0.470 6.755 5016 Z= 0.250 Chirality : 0.043 0.143 554 Planarity : 0.003 0.032 658 Dihedral : 7.545 79.326 515 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.46 % 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: 0.58 (0.60), residues: 79 loop : -1.00 (0.41), residues: 201 *********************** 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 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 18 time to evaluate : 0.432 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 31 average time/residue: 0.7647 time to fit residues: 25.3220 Evaluate side-chains 23 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.5958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 3703 Z= 0.239 Angle : 0.492 7.868 5016 Z= 0.262 Chirality : 0.044 0.213 554 Planarity : 0.003 0.043 658 Dihedral : 7.205 75.469 515 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.86 % 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: 0.00 (0.39), residues: 459 helix: 0.83 (0.39), residues: 185 sheet: 0.74 (0.62), residues: 72 loop : -1.03 (0.41), residues: 202 *********************** 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 29 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.430 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.8500 time to fit residues: 26.1324 Evaluate side-chains 21 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 269 ASN A 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 3703 Z= 0.301 Angle : 0.525 8.085 5016 Z= 0.279 Chirality : 0.045 0.163 554 Planarity : 0.004 0.044 658 Dihedral : 7.015 71.273 515 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.39 % 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: 0.12 (0.39), residues: 459 helix: 0.89 (0.39), residues: 187 sheet: 0.51 (0.59), residues: 82 loop : -0.89 (0.44), residues: 190 *********************** 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 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 30 average time/residue: 1.0647 time to fit residues: 33.5001 Evaluate side-chains 25 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1953 time to fit residues: 0.7998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.005 0.027 3703 Z= 0.303 Angle : 0.530 8.989 5016 Z= 0.279 Chirality : 0.045 0.143 554 Planarity : 0.004 0.047 658 Dihedral : 7.103 72.796 515 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.39 % 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: 0.16 (0.40), residues: 459 helix: 0.94 (0.39), residues: 187 sheet: 0.52 (0.59), residues: 82 loop : -0.87 (0.45), residues: 190 *********************** 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 31 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 1.0829 time to fit residues: 32.9168 Evaluate side-chains 27 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1834 time to fit residues: 0.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 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 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1362 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= 0.203 Angle : 0.495 9.122 5016 Z= 0.258 Chirality : 0.044 0.136 554 Planarity : 0.003 0.047 658 Dihedral : 6.925 71.033 515 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.39 % 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: 0.30 (0.40), residues: 459 helix: 1.06 (0.39), residues: 187 sheet: 0.49 (0.57), residues: 89 loop : -0.80 (0.46), residues: 183 *********************** 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 32 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 1.1385 time to fit residues: 36.9260 Evaluate side-chains 27 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1997 time to fit residues: 0.8405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3703 Z= 0.180 Angle : 0.493 9.396 5016 Z= 0.255 Chirality : 0.044 0.133 554 Planarity : 0.003 0.048 658 Dihedral : 6.812 68.708 515 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 2.13 % 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: 1.13 (0.40), residues: 185 sheet: 0.55 (0.57), residues: 89 loop : -0.80 (0.46), residues: 185 *********************** 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 30 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 1.2545 time to fit residues: 37.8944 Evaluate side-chains 26 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1702 time to fit residues: 0.6942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1417 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= 0.163 Angle : 0.484 9.530 5016 Z= 0.253 Chirality : 0.043 0.136 554 Planarity : 0.003 0.047 658 Dihedral : 6.670 66.233 515 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.86 % 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: 1.13 (0.39), residues: 185 sheet: 0.65 (0.57), residues: 87 loop : -0.84 (0.45), residues: 187 *********************** 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 29 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 28 average time/residue: 1.0859 time to fit residues: 31.9505 Evaluate side-chains 27 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2693 time to fit residues: 0.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0870 chunk 32 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3703 Z= 0.127 Angle : 0.472 9.693 5016 Z= 0.245 Chirality : 0.043 0.136 554 Planarity : 0.003 0.047 658 Dihedral : 6.373 62.657 515 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.60 % 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: 0.39 (0.40), residues: 459 helix: 1.19 (0.40), residues: 185 sheet: 0.48 (0.55), residues: 96 loop : -0.80 (0.47), residues: 178 *********************** 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 29 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 1.0358 time to fit residues: 31.6086 Evaluate side-chains 26 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.6174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.173 Angle : 0.519 13.621 5016 Z= 0.259 Chirality : 0.043 0.139 554 Planarity : 0.003 0.048 658 Dihedral : 6.297 60.878 515 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.60 % 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: 0.43 (0.40), residues: 459 helix: 1.20 (0.39), residues: 185 sheet: 0.69 (0.57), residues: 87 loop : -0.81 (0.45), residues: 187 ********************** 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 30 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 1.1088 time to fit residues: 34.8077 Evaluate side-chains 27 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 269 ASN A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053363 restraints weight = 12197.169| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.18 r_work: 0.3027 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 3703 Z= 0.251 Angle : 0.545 12.368 5016 Z= 0.278 Chirality : 0.044 0.140 554 Planarity : 0.004 0.048 658 Dihedral : 6.458 61.566 515 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.60 % 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: 0.44 (0.40), residues: 459 helix: 1.19 (0.40), residues: 185 sheet: 0.98 (0.59), residues: 77 loop : -0.83 (0.44), residues: 197 =============================================================================== Job complete usr+sys time: 1573.62 seconds wall clock time: 28 minutes 42.41 seconds (1722.41 seconds total)