Starting phenix.real_space_refine (version: dev) on Sun Dec 11 16:28:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/12_2022/8a8m_15233_updated.pdb" } resolution = 4.0 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 5244 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2816 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 17, 'TRANS': 331} Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASP A 177 " occ=0.78 ... (6 atoms not shown) pdb=" OD2 ASP A 177 " occ=0.78 Time building chain proxies: 3.47, per 1000 atoms: 0.66 Number of scatterers: 5244 At special positions: 0 Unit cell: (61.248, 81.026, 102.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 4 15.00 Mg 4 11.99 O 973 8.00 N 886 7.00 C 3348 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: 2.02 Conformation dependent library (CDL) restraints added in 716.4 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 5 sheets defined 36.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 113 through 119 removed outlier: 4.298A pdb=" N LYS A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 144 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 230 through 239 removed outlier: 4.118A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.028A pdb=" N TYR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.395A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.635A pdb=" N GLN A 310 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.059A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 90 through 105 removed outlier: 4.447A pdb=" N ARG B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.659A pdb=" N ASP B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 172 removed outlier: 3.745A pdb=" N LYS B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.914A pdb=" N SER B 319 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.544A pdb=" N LEU A 13 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.684A pdb=" N ILE B 41 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.899A pdb=" N ARG B 71 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 185 through 187 147 hydrogen bonds defined for protein. 423 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: 1.40 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1709 1.35 - 1.48: 1265 1.48 - 1.61: 2331 1.61 - 1.74: 2 1.74 - 1.87: 53 Bond restraints: 5360 Sorted by residual: bond pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.55e+00 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.27e-02 6.20e+03 2.06e+00 bond pdb=" N HIS A 312 " pdb=" CA HIS A 312 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.44e-02 4.82e+03 1.49e+00 bond pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.25e-02 6.40e+03 1.32e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.55: 154 105.55 - 112.70: 2797 112.70 - 119.85: 1835 119.85 - 126.99: 2408 126.99 - 134.14: 78 Bond angle restraints: 7272 Sorted by residual: angle pdb=" N LEU A 74 " pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.57e+01 angle pdb=" CA LYS B 329 " pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.81 118.62 -8.81 2.21e+00 2.05e-01 1.59e+01 angle pdb=" CA GLU B 68 " pdb=" CB GLU B 68 " pdb=" CG GLU B 68 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C ILE A 235 " pdb=" N LEU A 236 " pdb=" CA LEU A 236 " ideal model delta sigma weight residual 120.28 125.16 -4.88 1.34e+00 5.57e-01 1.33e+01 ... (remaining 7267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2731 17.80 - 35.61: 378 35.61 - 53.41: 88 53.41 - 71.21: 20 71.21 - 89.02: 9 Dihedral angle restraints: 3226 sinusoidal: 1331 harmonic: 1895 Sorted by residual: dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N MET A 109 " pdb=" CA MET A 109 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N MET B 132 " pdb=" CA MET B 132 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 3223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 565 0.043 - 0.087: 186 0.087 - 0.130: 49 0.130 - 0.173: 10 0.173 - 0.217: 4 Chirality restraints: 814 Sorted by residual: chirality pdb=" CA LEU B 267 " pdb=" N LEU B 267 " pdb=" C LEU B 267 " pdb=" CB LEU B 267 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA TYR B 305 " pdb=" N TYR B 305 " pdb=" C TYR B 305 " pdb=" CB TYR B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 811 not shown) Planarity restraints: 920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 68 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CD GLU B 68 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 68 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 68 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 152 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO A 153 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 150 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 151 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.024 5.00e-02 4.00e+02 ... (remaining 917 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 737 2.75 - 3.29: 5816 3.29 - 3.83: 9246 3.83 - 4.36: 10936 4.36 - 4.90: 16821 Nonbonded interactions: 43556 Sorted by model distance: nonbonded pdb=" O SER B 235 " pdb=" OG SER B 238 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR B 140 " pdb=" OE1 GLU B 249 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU A 215 " pdb=" OG1 THR A 221 " model vdw 2.233 2.440 nonbonded pdb=" O ASP A 205 " pdb=" OG SER A 208 " model vdw 2.240 2.440 nonbonded pdb=" NH2 ARG B 178 " pdb=" O TYR B 203 " model vdw 2.243 2.520 ... (remaining 43551 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 4 5.21 5 S 29 5.16 5 C 3348 2.51 5 N 886 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.78 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 13.150 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5360 Z= 0.233 Angle : 0.888 9.558 7272 Z= 0.471 Chirality : 0.048 0.217 814 Planarity : 0.005 0.050 920 Dihedral : 17.750 89.016 1998 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer Outliers : 1.56 % 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: -2.63 (0.31), residues: 639 helix: -0.84 (0.34), residues: 219 sheet: -2.27 (0.64), residues: 53 loop : -2.31 (0.31), residues: 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.1703 time to fit residues: 20.5004 Evaluate side-chains 71 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0639 time to fit residues: 1.1946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 26 optimal weight: 0.0270 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.0670 chunk 25 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 45 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 265 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5360 Z= 0.205 Angle : 0.759 9.207 7272 Z= 0.380 Chirality : 0.047 0.180 814 Planarity : 0.005 0.050 920 Dihedral : 6.501 55.037 705 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 2.60 % 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: -2.40 (0.31), residues: 639 helix: -0.56 (0.34), residues: 220 sheet: -2.36 (0.69), residues: 46 loop : -2.22 (0.30), residues: 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 0.1399 time to fit residues: 15.2941 Evaluate side-chains 73 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0859 time to fit residues: 1.7882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN B 266 GLN B 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 5360 Z= 0.317 Angle : 0.813 9.023 7272 Z= 0.415 Chirality : 0.049 0.183 814 Planarity : 0.005 0.047 920 Dihedral : 6.552 53.222 705 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 39.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer Outliers : 5.03 % 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: -2.56 (0.31), residues: 639 helix: -0.78 (0.33), residues: 228 sheet: -2.94 (0.66), residues: 46 loop : -2.20 (0.31), residues: 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 90 average time/residue: 0.1460 time to fit residues: 17.8115 Evaluate side-chains 81 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0546 time to fit residues: 2.3196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 5360 Z= 0.331 Angle : 0.858 11.658 7272 Z= 0.433 Chirality : 0.051 0.276 814 Planarity : 0.006 0.048 920 Dihedral : 6.802 56.452 705 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 44.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer Outliers : 5.38 % 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: -2.88 (0.30), residues: 639 helix: -1.19 (0.31), residues: 229 sheet: -2.73 (0.58), residues: 61 loop : -2.29 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 93 average time/residue: 0.1778 time to fit residues: 21.5461 Evaluate side-chains 83 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0812 time to fit residues: 2.9293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 228 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 5360 Z= 0.204 Angle : 0.808 10.966 7272 Z= 0.396 Chirality : 0.047 0.253 814 Planarity : 0.005 0.048 920 Dihedral : 6.699 57.718 705 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 29.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer Outliers : 1.91 % 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: -2.58 (0.31), residues: 639 helix: -0.79 (0.33), residues: 229 sheet: -2.83 (0.58), residues: 58 loop : -2.19 (0.31), residues: 352 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 77 average time/residue: 0.1848 time to fit residues: 18.8706 Evaluate side-chains 66 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0619 time to fit residues: 1.2905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 58 optimal weight: 0.2980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5360 Z= 0.217 Angle : 0.796 9.167 7272 Z= 0.393 Chirality : 0.047 0.316 814 Planarity : 0.005 0.054 920 Dihedral : 6.589 53.870 705 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 33.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer Outliers : 2.43 % 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: -2.52 (0.32), residues: 639 helix: -0.87 (0.32), residues: 236 sheet: -2.72 (0.60), residues: 58 loop : -2.09 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.1743 time to fit residues: 17.3765 Evaluate side-chains 65 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0497 time to fit residues: 1.2747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5360 Z= 0.259 Angle : 0.842 10.940 7272 Z= 0.405 Chirality : 0.048 0.324 814 Planarity : 0.005 0.056 920 Dihedral : 6.566 50.086 705 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 37.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 0.87 % 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: -2.47 (0.32), residues: 639 helix: -0.87 (0.33), residues: 234 sheet: -2.82 (0.59), residues: 58 loop : -1.99 (0.33), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.1913 time to fit residues: 16.2797 Evaluate side-chains 61 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0650 time to fit residues: 1.1084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 0.0010 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5360 Z= 0.196 Angle : 0.829 10.413 7272 Z= 0.394 Chirality : 0.049 0.380 814 Planarity : 0.005 0.051 920 Dihedral : 6.468 48.379 705 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.82 % Favored : 92.02 % Rotamer Outliers : 0.87 % 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: -2.39 (0.33), residues: 639 helix: -0.77 (0.34), residues: 233 sheet: -3.10 (0.63), residues: 48 loop : -1.95 (0.33), residues: 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1894 time to fit residues: 16.5045 Evaluate side-chains 66 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0509 time to fit residues: 1.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 5360 Z= 0.328 Angle : 0.875 10.550 7272 Z= 0.437 Chirality : 0.050 0.332 814 Planarity : 0.005 0.057 920 Dihedral : 6.503 43.635 705 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 46.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.17 % Favored : 89.67 % Rotamer Outliers : 1.04 % 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: -2.66 (0.31), residues: 639 helix: -1.11 (0.32), residues: 233 sheet: -3.30 (0.57), residues: 58 loop : -1.96 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1921 time to fit residues: 16.8132 Evaluate side-chains 66 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1318 time to fit residues: 1.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5360 Z= 0.215 Angle : 0.888 11.406 7272 Z= 0.426 Chirality : 0.051 0.368 814 Planarity : 0.005 0.049 920 Dihedral : 6.529 43.453 705 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 34.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.08 % Favored : 90.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.57 (0.32), residues: 639 helix: -0.99 (0.32), residues: 233 sheet: -3.30 (0.58), residues: 60 loop : -1.91 (0.33), residues: 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1902 time to fit residues: 15.8854 Evaluate side-chains 64 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.107004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.074717 restraints weight = 24462.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.076266 restraints weight = 20657.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.077456 restraints weight = 18224.148| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 5360 Z= 0.312 Angle : 0.894 11.151 7272 Z= 0.442 Chirality : 0.050 0.285 814 Planarity : 0.005 0.053 920 Dihedral : 6.626 39.945 705 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 45.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.36 % Rotamer Outliers : 1.04 % 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: -2.64 (0.31), residues: 639 helix: -1.09 (0.32), residues: 231 sheet: -3.42 (0.56), residues: 60 loop : -1.90 (0.33), residues: 348 =============================================================================== Job complete usr+sys time: 1434.34 seconds wall clock time: 26 minutes 57.44 seconds (1617.44 seconds total)