Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 18:16:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj3_34831/07_2023/8hj3_34831_neut_updated.pdb" } resolution = 3.29 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= 0.001 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 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3274 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 419 "'] Classifications: {'peptide': 416, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395, None: 1} Not linked: pdbres="LYS A 419 " pdbres="NAP A 501 " Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 2.21, per 1000 atoms: 0.68 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 71.978, 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 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 1.39 Conformation dependent library (CDL) restraints added in 470.8 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 48.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 4.117A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.774A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.654A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.599A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.482A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.418A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.970A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 167 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1062 1.34 - 1.46: 724 1.46 - 1.58: 1533 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" N LYS A 389 " pdb=" CA LYS A 389 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.61e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" N HIS A 388 " pdb=" CA HIS A 388 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.37e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.24: 64 104.24 - 111.68: 1575 111.68 - 119.12: 1183 119.12 - 126.55: 1667 126.55 - 133.99: 72 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C TRP A 89 " pdb=" N MET A 90 " pdb=" CA MET A 90 " ideal model delta sigma weight residual 121.58 114.33 7.25 1.95e+00 2.63e-01 1.38e+01 angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 106.80 7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N MET A 90 " pdb=" CA MET A 90 " pdb=" CB MET A 90 " ideal model delta sigma weight residual 110.41 116.33 -5.92 1.68e+00 3.54e-01 1.24e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 115.58 -4.71 1.54e+00 4.22e-01 9.37e+00 angle pdb=" CA MET A 90 " pdb=" CB MET A 90 " pdb=" CG MET A 90 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.01e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1786 17.65 - 35.29: 151 35.29 - 52.94: 38 52.94 - 70.59: 7 70.59 - 88.23: 4 Dihedral angle restraints: 1986 sinusoidal: 797 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 90 " pdb=" C MET A 90 " pdb=" N THR A 91 " pdb=" CA THR A 91 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -88.23 88.23 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 1983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 346 0.040 - 0.081: 99 0.081 - 0.121: 55 0.121 - 0.161: 0 0.161 - 0.202: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA MET A 90 " pdb=" N MET A 90 " pdb=" C MET A 90 " pdb=" CB MET A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " 0.053 2.00e-02 2.50e+03 7.24e-02 1.05e+02 pdb=" C2N NAP A 501 " -0.128 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.046 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.036 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 142 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 197 " -0.013 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE A 197 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 197 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 197 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 197 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 197 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 197 " -0.000 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 362 2.74 - 3.28: 3497 3.28 - 3.82: 5991 3.82 - 4.36: 6980 4.36 - 4.90: 11719 Nonbonded interactions: 28549 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" NE2 GLN A 337 " model vdw 2.200 2.520 nonbonded pdb=" NH1 ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.253 2.520 nonbonded pdb=" O TYR A 20 " pdb=" NZ LYS A 391 " model vdw 2.264 2.520 nonbonded pdb=" O ILE A 309 " pdb=" NZ LYS A 333 " model vdw 2.286 2.520 nonbonded pdb=" N GLU A 325 " pdb=" OE1 GLU A 325 " model vdw 2.298 2.520 ... (remaining 28544 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: 0.690 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: 3.530 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.120 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.122 3351 Z= 0.378 Angle : 0.802 7.569 4561 Z= 0.454 Chirality : 0.046 0.202 501 Planarity : 0.005 0.072 579 Dihedral : 14.916 88.231 1228 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 414 helix: 1.79 (0.35), residues: 206 sheet: 0.24 (0.68), residues: 64 loop : -0.31 (0.53), residues: 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1342 time to fit residues: 11.1685 Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.201 Angle : 0.546 8.514 4561 Z= 0.288 Chirality : 0.044 0.196 501 Planarity : 0.004 0.052 579 Dihedral : 8.392 63.452 471 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.41), residues: 414 helix: 1.94 (0.35), residues: 205 sheet: 0.30 (0.67), residues: 64 loop : -0.45 (0.52), residues: 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.1289 time to fit residues: 10.5705 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0785 time to fit residues: 0.9715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.203 Angle : 0.547 8.341 4561 Z= 0.288 Chirality : 0.043 0.195 501 Planarity : 0.004 0.052 579 Dihedral : 8.056 58.741 471 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.41), residues: 414 helix: 1.97 (0.34), residues: 204 sheet: 0.14 (0.68), residues: 66 loop : -0.55 (0.51), residues: 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1331 time to fit residues: 10.1617 Evaluate side-chains 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0457 time to fit residues: 0.9128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.222 Angle : 0.547 8.695 4561 Z= 0.292 Chirality : 0.044 0.207 501 Planarity : 0.004 0.050 579 Dihedral : 7.234 59.663 471 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.41), residues: 414 helix: 1.96 (0.35), residues: 204 sheet: 0.07 (0.68), residues: 66 loop : -0.63 (0.51), residues: 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1265 time to fit residues: 9.4851 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0426 time to fit residues: 0.5600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 3351 Z= 0.300 Angle : 0.604 9.043 4561 Z= 0.321 Chirality : 0.044 0.215 501 Planarity : 0.004 0.051 579 Dihedral : 6.909 57.174 471 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.42), residues: 414 helix: 1.87 (0.35), residues: 204 sheet: -0.09 (0.68), residues: 66 loop : -0.57 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.379 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1326 time to fit residues: 9.5059 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0347 time to fit residues: 0.7427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3351 Z= 0.191 Angle : 0.559 9.390 4561 Z= 0.296 Chirality : 0.043 0.216 501 Planarity : 0.004 0.049 579 Dihedral : 6.861 59.935 471 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.41), residues: 414 helix: 1.99 (0.35), residues: 204 sheet: -0.11 (0.66), residues: 66 loop : -0.61 (0.51), residues: 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.386 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.1234 time to fit residues: 9.7586 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0361 time to fit residues: 0.5223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3351 Z= 0.297 Angle : 0.622 9.909 4561 Z= 0.328 Chirality : 0.045 0.221 501 Planarity : 0.004 0.050 579 Dihedral : 6.779 58.024 471 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.41), residues: 414 helix: 1.79 (0.35), residues: 204 sheet: -0.13 (0.67), residues: 66 loop : -0.66 (0.52), residues: 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.1319 time to fit residues: 9.6889 Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0433 time to fit residues: 0.7865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3351 Z= 0.191 Angle : 0.595 10.560 4561 Z= 0.312 Chirality : 0.044 0.224 501 Planarity : 0.004 0.048 579 Dihedral : 6.359 53.867 471 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.42), residues: 414 helix: 1.70 (0.35), residues: 209 sheet: 0.05 (0.67), residues: 66 loop : -0.63 (0.53), residues: 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.406 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.1390 time to fit residues: 10.4720 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0384 time to fit residues: 0.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 3351 Z= 0.304 Angle : 0.673 11.028 4561 Z= 0.353 Chirality : 0.046 0.212 501 Planarity : 0.004 0.048 579 Dihedral : 6.420 52.511 471 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.42), residues: 414 helix: 1.61 (0.36), residues: 206 sheet: -0.03 (0.67), residues: 66 loop : -0.59 (0.53), residues: 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.457 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1486 time to fit residues: 10.0772 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0439 time to fit residues: 0.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.215 Angle : 0.641 10.562 4561 Z= 0.336 Chirality : 0.045 0.224 501 Planarity : 0.004 0.048 579 Dihedral : 6.067 48.519 471 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.42), residues: 414 helix: 1.61 (0.35), residues: 209 sheet: 0.11 (0.68), residues: 66 loop : -0.80 (0.53), residues: 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1498 time to fit residues: 10.8141 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 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: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.122215 restraints weight = 8102.743| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.83 r_work: 0.3603 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3351 Z= 0.281 Angle : 0.625 8.919 4561 Z= 0.326 Chirality : 0.045 0.194 501 Planarity : 0.004 0.048 579 Dihedral : 6.068 47.547 471 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.42), residues: 414 helix: 1.55 (0.35), residues: 209 sheet: 0.08 (0.68), residues: 66 loop : -0.81 (0.54), residues: 139 =============================================================================== Job complete usr+sys time: 1050.16 seconds wall clock time: 19 minutes 43.80 seconds (1183.80 seconds total)