Starting phenix.real_space_refine on Fri Jul 19 07:18:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/07_2024/8uc0_42111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/07_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_42111/07_2024/8uc0_42111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/07_2024/8uc0_42111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/07_2024/8uc0_42111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc0_42111/07_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-5388/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: 4.93, per 1000 atoms: 0.72 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: 6.05 Conformation dependent library (CDL) restraints added in 602.4 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: 0.46 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: 6.32 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 1.850 nonbonded pdb=" OD1 ASP A 393 " pdb="HH11 ARG A 517 " model vdw 1.717 1.850 nonbonded pdb=" O ILE A 130 " pdb="HD22 ASN A 356 " model vdw 1.717 1.850 nonbonded pdb=" O SER A 104 " pdb="HH11 ARG A 107 " model vdw 1.733 1.850 nonbonded pdb=" OE1 GLU A 318 " pdb=" H GLU A 318 " model vdw 1.777 1.850 ... (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: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.620 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- 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 : 0.560 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 2.1545 time to fit residues: 102.8863 Evaluate side-chains 38 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 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: 0.8925 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3477 Z= 0.211 Angle : 0.511 6.102 4760 Z= 0.274 Chirality : 0.035 0.129 573 Planarity : 0.004 0.038 563 Dihedral : 5.898 59.100 668 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 3.87 (0.41), residues: 420 helix: 3.12 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -0.88 (0.80), residues: 66 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 0.012 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 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 40 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.519 Fit side-chains REVERT: A 171 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7776 (mpt90) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 1.9588 time to fit residues: 77.8301 Evaluate side-chains 37 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8979 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3477 Z= 0.213 Angle : 0.505 6.124 4760 Z= 0.269 Chirality : 0.035 0.136 573 Planarity : 0.004 0.039 563 Dihedral : 5.930 57.610 666 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 3.71 (0.41), residues: 420 helix: 3.01 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -0.91 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.001 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 39 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.555 Fit side-chains REVERT: A 171 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7506 (mpt90) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 2.0905 time to fit residues: 82.8370 Evaluate side-chains 37 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 267 THR 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: 0.9980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8990 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3477 Z= 0.207 Angle : 0.497 6.148 4760 Z= 0.267 Chirality : 0.035 0.134 573 Planarity : 0.004 0.039 563 Dihedral : 6.007 55.849 666 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.84 % Allowed : 13.73 % Favored : 85.43 % 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: 3.56 (0.41), residues: 420 helix: 2.95 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.11 (0.74), 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 0.002 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 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.525 Fit side-chains REVERT: A 171 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7614 (mpt90) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 2.1455 time to fit residues: 78.2172 Evaluate side-chains 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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: 0.8965 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3477 Z= 0.145 Angle : 0.470 6.048 4760 Z= 0.250 Chirality : 0.034 0.126 573 Planarity : 0.004 0.040 563 Dihedral : 5.834 56.510 666 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 3.66 (0.41), residues: 420 helix: 2.97 (0.26), residues: 352 sheet: None (None), residues: 0 loop : -0.78 (0.80), residues: 68 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 223 *********************** 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 38 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.526 Fit side-chains REVERT: A 171 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7450 (mpt90) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 2.0797 time to fit residues: 80.1896 Evaluate side-chains 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 267 THR 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: 0.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.9004 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3477 Z= 0.229 Angle : 0.500 6.171 4760 Z= 0.268 Chirality : 0.035 0.133 573 Planarity : 0.004 0.039 563 Dihedral : 6.089 59.585 666 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.84 % Allowed : 13.17 % 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: 3.60 (0.41), residues: 420 helix: 2.96 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.90 (0.76), residues: 70 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 0.017 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 *********************** 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: 3 poor density : 30 time to evaluate : 0.468 Fit side-chains REVERT: A 171 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7599 (mpt90) outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 2.1374 time to fit residues: 71.1438 Evaluate side-chains 33 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8981 moved from start: 0.2345 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= 0.154 Angle : 0.474 6.059 4760 Z= 0.252 Chirality : 0.034 0.127 573 Planarity : 0.004 0.040 563 Dihedral : 5.938 59.088 666 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 3.62 (0.41), residues: 420 helix: 2.96 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.88 (0.79), residues: 68 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 0.013 0.001 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 *********************** 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 : 0.577 Fit side-chains REVERT: A 171 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7423 (mpt90) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 2.3232 time to fit residues: 79.9801 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 267 THR 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: 0.9980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 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: 0.8997 moved from start: 0.2438 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= 0.195 Angle : 0.486 6.137 4760 Z= 0.259 Chirality : 0.034 0.130 573 Planarity : 0.004 0.040 563 Dihedral : 5.990 58.218 666 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 3.60 (0.41), residues: 420 helix: 2.97 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.99 (0.75), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 223 *********************** 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 : 0.480 Fit side-chains REVERT: A 171 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7574 (mpt90) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 1.7808 time to fit residues: 58.0498 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 267 THR 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: 0.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8996 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3477 Z= 0.187 Angle : 0.487 6.126 4760 Z= 0.259 Chirality : 0.035 0.129 573 Planarity : 0.004 0.038 563 Dihedral : 5.981 57.115 666 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.40 % Allowed : 13.17 % Favored : 85.43 % 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: 3.58 (0.41), residues: 420 helix: 2.96 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.99 (0.76), residues: 70 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 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 *********************** 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 33 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.638 Fit side-chains REVERT: A 171 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7502 (mpt90) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 1.7579 time to fit residues: 59.3659 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 267 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: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 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: 0.8993 moved from start: 0.2497 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= 0.178 Angle : 0.487 6.128 4760 Z= 0.257 Chirality : 0.034 0.129 573 Planarity : 0.004 0.037 563 Dihedral : 5.955 56.767 666 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.40 % Allowed : 13.17 % Favored : 85.43 % 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: 3.57 (0.41), residues: 420 helix: 2.96 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -1.04 (0.75), residues: 70 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 223 ********************** 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 34 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.547 Fit side-chains REVERT: A 171 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7476 (mpt90) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 1.6677 time to fit residues: 58.2065 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 267 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: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.094242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076572 restraints weight = 15780.965| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.77 r_work: 0.2986 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3477 Z= 0.150 Angle : 0.482 6.067 4760 Z= 0.252 Chirality : 0.034 0.127 573 Planarity : 0.004 0.038 563 Dihedral : 5.860 57.391 666 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.12 % Allowed : 14.29 % 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: 3.59 (0.41), residues: 420 helix: 2.95 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.97 (0.78), residues: 68 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 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.99 seconds wall clock time: 56 minutes 23.79 seconds (3383.79 seconds total)