Starting phenix.real_space_refine on Sat Aug 3 04:20:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/08_2024/8uc0_42111.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 S 18 5.16 5 C 2274 2.51 5 N 508 2.21 5 O 686 1.98 5 H 3375 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6654 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 403} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 207 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3, 'water': 102} Link IDs: {None: 104} Time building chain proxies: 4.86, per 1000 atoms: 0.71 Number of scatterers: 6861 At special positions: 0 Unit cell: (87, 57.275, 65.975, 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 18 16.00 O 686 8.00 N 508 7.00 C 2274 6.00 H 3375 1.00 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: 5.63 Conformation dependent library (CDL) restraints added in 688.4 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.762A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.738A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.157A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.829A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.618A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.346A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.623A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.656A pdb=" N ASN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.008A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 397 through 420 removed outlier: 3.698A pdb=" N THR A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 489 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.783A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 837 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: 2.25 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3367 1.03 - 1.23: 11 1.23 - 1.42: 1404 1.42 - 1.62: 2042 1.62 - 1.81: 28 Bond restraints: 6852 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.07e+00 bond pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 5.99e-01 bond pdb=" CB TRP A 391 " pdb=" CG TRP A 391 " ideal model delta sigma weight residual 1.498 1.519 -0.021 3.10e-02 1.04e+03 4.48e-01 bond pdb=" C PHE A 162 " pdb=" O PHE A 162 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 4.36e-01 bond pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.28e-01 ... (remaining 6847 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 124 106.82 - 113.61: 8060 113.61 - 120.40: 2407 120.40 - 127.19: 1752 127.19 - 133.98: 37 Bond angle restraints: 12380 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.31 -3.10 1.07e+00 8.73e-01 8.41e+00 angle pdb=" CA TYR A 117 " pdb=" CB TYR A 117 " pdb=" CG TYR A 117 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.35e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.18 -5.37 2.21e+00 2.05e-01 5.90e+00 angle pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 118.44 121.96 -3.52 1.59e+00 3.96e-01 4.90e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.91 2.31 1.12e+00 7.97e-01 4.24e+00 ... (remaining 12375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.00: 2902 13.00 - 26.00: 303 26.00 - 39.00: 87 39.00 - 52.00: 54 52.00 - 65.00: 49 Dihedral angle restraints: 3395 sinusoidal: 1906 harmonic: 1489 Sorted by residual: dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual 180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" N THR A 203 " pdb=" CA THR A 203 " pdb=" CB THR A 203 " pdb=" OG1 THR A 203 " ideal model delta sinusoidal sigma weight residual -180.00 -120.53 -59.47 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 326 " pdb=" CB ARG A 326 " pdb=" CG ARG A 326 " pdb=" CD ARG A 326 " ideal model delta sinusoidal sigma weight residual -180.00 -122.45 -57.55 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 377 0.022 - 0.043: 100 0.043 - 0.065: 42 0.065 - 0.087: 46 0.087 - 0.109: 8 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE A 131 " pdb=" N ILE A 131 " pdb=" C ILE A 131 " pdb=" CB ILE A 131 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.66e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 570 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 332 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 333 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C PHE A 114 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 123 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C PHE A 123 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE A 123 " -0.007 2.00e-02 2.50e+03 pdb=" N GLN A 124 " -0.006 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 717 2.24 - 2.83: 15820 2.83 - 3.42: 19749 3.42 - 4.01: 26710 4.01 - 4.60: 40779 Nonbonded interactions: 103775 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" HG1 THR A 419 " model vdw 1.653 2.450 nonbonded pdb=" OD1 ASP A 393 " pdb="HH11 ARG A 517 " model vdw 1.717 2.450 nonbonded pdb=" O ILE A 130 " pdb="HD22 ASN A 356 " model vdw 1.717 2.450 nonbonded pdb=" O SER A 104 " pdb="HH11 ARG A 107 " model vdw 1.733 2.450 nonbonded pdb=" OE1 GLU A 318 " pdb=" H GLU A 318 " model vdw 1.777 2.450 ... (remaining 103770 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: 0.010 Normalize map: mean=0, sd=1: 4.160 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.570 Find NCS groups from input model: 0.050 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 : 0.002 0.021 3477 Z= 0.130 Angle : 0.474 5.369 4760 Z= 0.266 Chirality : 0.032 0.109 573 Planarity : 0.003 0.040 563 Dihedral : 13.633 65.004 1381 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.84 % Allowed : 11.20 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.55 (0.41), residues: 420 helix: 3.04 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.31 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.526 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 2.1110 time to fit residues: 100.8244 Evaluate side-chains 38 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 282 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3477 Z= 0.245 Angle : 0.543 6.291 4760 Z= 0.291 Chirality : 0.035 0.131 573 Planarity : 0.004 0.037 563 Dihedral : 5.984 56.001 668 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.12 % Allowed : 12.32 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.78 (0.41), residues: 420 helix: 3.04 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -0.83 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.001 HIS A 145 PHE 0.014 0.002 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.545 Fit side-chains REVERT: A 171 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7727 (mpt90) REVERT: A 312 GLN cc_start: 0.7146 (mt0) cc_final: 0.6884 (mt0) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 2.0271 time to fit residues: 84.4752 Evaluate side-chains 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 516 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3477 Z= 0.255 Angle : 0.527 6.246 4760 Z= 0.284 Chirality : 0.036 0.137 573 Planarity : 0.004 0.037 563 Dihedral : 6.169 55.477 666 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.40 % Allowed : 12.61 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.46 (0.41), residues: 420 helix: 2.81 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -1.01 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.016 0.002 PHE A 114 TYR 0.023 0.002 TYR A 117 ARG 0.002 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.527 Fit side-chains REVERT: A 171 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7574 (mpt90) REVERT: A 312 GLN cc_start: 0.7147 (mt0) cc_final: 0.6926 (mt0) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 2.0481 time to fit residues: 74.7906 Evaluate side-chains 35 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3477 Z= 0.198 Angle : 0.503 6.171 4760 Z= 0.270 Chirality : 0.035 0.130 573 Planarity : 0.004 0.037 563 Dihedral : 6.089 59.917 666 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.12 % Allowed : 12.61 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.45 (0.41), residues: 420 helix: 2.90 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.27 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.527 Fit side-chains REVERT: A 171 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7603 (mpt90) REVERT: A 312 GLN cc_start: 0.7133 (mt0) cc_final: 0.6916 (mt0) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 2.0794 time to fit residues: 71.5331 Evaluate side-chains 35 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3477 Z= 0.202 Angle : 0.496 6.175 4760 Z= 0.266 Chirality : 0.035 0.130 573 Planarity : 0.004 0.037 563 Dihedral : 6.065 57.949 666 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.12 % Allowed : 12.32 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.41 (0.41), residues: 420 helix: 2.84 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.22 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.016 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.563 Fit side-chains REVERT: A 171 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7535 (mpt90) REVERT: A 312 GLN cc_start: 0.7152 (mt0) cc_final: 0.6927 (mt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 2.0521 time to fit residues: 72.7489 Evaluate side-chains 33 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3477 Z= 0.193 Angle : 0.496 6.181 4760 Z= 0.266 Chirality : 0.035 0.130 573 Planarity : 0.004 0.037 563 Dihedral : 6.040 56.593 666 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 12.89 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.43 (0.41), residues: 420 helix: 2.88 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.28 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.537 Fit side-chains REVERT: A 171 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7512 (mpt90) REVERT: A 312 GLN cc_start: 0.7129 (mt0) cc_final: 0.6912 (mt0) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 2.2091 time to fit residues: 71.2405 Evaluate side-chains 33 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3477 Z= 0.179 Angle : 0.486 6.155 4760 Z= 0.260 Chirality : 0.034 0.128 573 Planarity : 0.004 0.038 563 Dihedral : 5.993 56.105 666 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 13.17 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.41 (0.41), residues: 420 helix: 2.85 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.31 (0.70), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.014 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.530 Fit side-chains REVERT: A 171 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7480 (mpt90) REVERT: A 312 GLN cc_start: 0.7110 (mt0) cc_final: 0.6873 (mt0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 2.2242 time to fit residues: 74.1108 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3477 Z= 0.196 Angle : 0.494 6.182 4760 Z= 0.264 Chirality : 0.035 0.129 573 Planarity : 0.004 0.038 563 Dihedral : 6.027 56.279 666 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 13.17 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.41 (0.40), residues: 420 helix: 2.89 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.39 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.555 Fit side-chains REVERT: A 171 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7550 (mpt90) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 1.8958 time to fit residues: 59.6756 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3477 Z= 0.148 Angle : 0.479 6.104 4760 Z= 0.254 Chirality : 0.034 0.125 573 Planarity : 0.004 0.038 563 Dihedral : 5.907 55.932 666 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.44 (0.41), residues: 420 helix: 2.88 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.35 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.536 Fit side-chains REVERT: A 171 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7384 (mpt90) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 1.7660 time to fit residues: 57.5744 Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 0.0060 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3477 Z= 0.149 Angle : 0.480 6.058 4760 Z= 0.254 Chirality : 0.034 0.124 573 Planarity : 0.004 0.038 563 Dihedral : 5.854 57.119 666 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.84 % Allowed : 14.57 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.50 (0.41), residues: 420 helix: 2.92 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -1.33 (0.72), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.544 Fit side-chains REVERT: A 171 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7375 (mpt90) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 1.9197 time to fit residues: 60.3992 Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.076168 restraints weight = 15971.554| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.76 r_work: 0.3039 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3477 Z= 0.164 Angle : 0.487 6.045 4760 Z= 0.257 Chirality : 0.034 0.124 573 Planarity : 0.004 0.038 563 Dihedral : 5.878 57.620 666 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.84 % Allowed : 14.85 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.48 (0.41), residues: 420 helix: 2.92 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.40 (0.70), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.014 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.77 seconds wall clock time: 58 minutes 5.96 seconds (3485.96 seconds total)