Starting phenix.real_space_refine on Wed Mar 12 00:10:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_42111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_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/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_42111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_42111.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_42111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc0_42111/03_2025/8uc0_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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.75, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 539.6 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: 0.56 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: 2.29 Time building geometry restraints manager: 2.29 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: 0.00 - 1.07: 11676 1.07 - 2.15: 653 2.15 - 3.22: 36 3.22 - 4.29: 11 4.29 - 5.37: 4 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: 0.000 Normalize map: mean=0, sd=1: 4.180 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: 0.140 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.050 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.496 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 2.1899 time to fit residues: 104.6053 Evaluate side-chains 38 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078750 restraints weight = 15670.458| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.73 r_work: 0.3034 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.524 Fit side-chains REVERT: A 171 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7483 (mpt90) REVERT: A 312 GLN cc_start: 0.6953 (mt0) cc_final: 0.6690 (mt0) REVERT: A 421 ASP cc_start: 0.8516 (p0) cc_final: 0.8228 (p0) REVERT: A 448 GLU cc_start: 0.8485 (tt0) cc_final: 0.8143 (tt0) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 2.0627 time to fit residues: 86.0159 Evaluate side-chains 38 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.093049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075138 restraints weight = 16084.467| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.77 r_work: 0.3019 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3477 Z= 0.247 Angle : 0.517 6.200 4760 Z= 0.278 Chirality : 0.035 0.133 573 Planarity : 0.004 0.037 563 Dihedral : 6.070 53.414 666 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 12.32 % 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: 3.59 (0.41), residues: 420 helix: 2.89 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -0.86 (0.83), 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 0.017 0.002 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 372 *********************** 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 to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.492 Fit side-chains REVERT: A 171 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7340 (mpt90) REVERT: A 312 GLN cc_start: 0.6935 (mt0) cc_final: 0.6687 (mt0) REVERT: A 448 GLU cc_start: 0.8538 (tt0) cc_final: 0.8205 (tt0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 2.0081 time to fit residues: 75.3982 Evaluate side-chains 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.092530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074675 restraints weight = 16334.594| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.78 r_work: 0.3021 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3477 Z= 0.225 Angle : 0.510 6.200 4760 Z= 0.275 Chirality : 0.035 0.132 573 Planarity : 0.004 0.037 563 Dihedral : 6.131 59.089 666 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 3.46 (0.41), residues: 420 helix: 2.89 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.12 (0.76), 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 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 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.535 Fit side-chains REVERT: A 171 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7406 (mpt90) REVERT: A 421 ASP cc_start: 0.8553 (p0) cc_final: 0.8224 (p0) REVERT: A 448 GLU cc_start: 0.8547 (tt0) cc_final: 0.8276 (tt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 2.1206 time to fit residues: 77.3617 Evaluate side-chains 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.092213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.074617 restraints weight = 16076.268| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.75 r_work: 0.3017 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2311 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 : 0.502 6.209 4760 Z= 0.270 Chirality : 0.035 0.132 573 Planarity : 0.004 0.037 563 Dihedral : 6.128 57.828 666 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 2.87 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.18 (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 0.016 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 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 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.517 Fit side-chains REVERT: A 171 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7380 (mpt90) REVERT: A 421 ASP cc_start: 0.8552 (p0) cc_final: 0.8246 (p0) REVERT: A 448 GLU cc_start: 0.8573 (tt0) cc_final: 0.8300 (tt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 2.1539 time to fit residues: 78.4733 Evaluate side-chains 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.091131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073539 restraints weight = 16214.617| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.76 r_work: 0.2988 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2469 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= 0.244 Angle : 0.513 6.303 4760 Z= 0.276 Chirality : 0.036 0.134 573 Planarity : 0.004 0.037 563 Dihedral : 6.226 56.495 666 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 3.35 (0.41), residues: 420 helix: 2.82 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.22 (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 0.017 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 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 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.478 Fit side-chains REVERT: A 171 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7408 (mpt90) REVERT: A 448 GLU cc_start: 0.8570 (tt0) cc_final: 0.8293 (tt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 2.2416 time to fit residues: 79.3743 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.092470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074845 restraints weight = 15970.467| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.76 r_work: 0.3012 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2455 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= 0.182 Angle : 0.496 6.245 4760 Z= 0.266 Chirality : 0.035 0.128 573 Planarity : 0.004 0.037 563 Dihedral : 6.116 55.906 666 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 13.45 % 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: 3.42 (0.41), residues: 420 helix: 2.87 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.20 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.567 Fit side-chains REVERT: A 154 MET cc_start: 0.8732 (mtt) cc_final: 0.8444 (mtt) REVERT: A 171 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7258 (mpt90) REVERT: A 421 ASP cc_start: 0.8516 (p0) cc_final: 0.8246 (p0) REVERT: A 448 GLU cc_start: 0.8561 (tt0) cc_final: 0.8296 (tt0) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 2.2056 time to fit residues: 75.7280 Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.091767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.074088 restraints weight = 16180.864| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.77 r_work: 0.3003 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2499 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= 0.209 Angle : 0.501 6.251 4760 Z= 0.268 Chirality : 0.035 0.129 573 Planarity : 0.004 0.037 563 Dihedral : 6.140 56.543 666 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 13.45 % 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: 3.38 (0.40), residues: 420 helix: 2.85 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.30 (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 0.016 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** 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 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.536 Fit side-chains REVERT: A 171 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7386 (mpt90) REVERT: A 421 ASP cc_start: 0.8521 (p0) cc_final: 0.8291 (p0) REVERT: A 448 GLU cc_start: 0.8538 (tt0) cc_final: 0.8274 (tt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 2.1612 time to fit residues: 76.5117 Evaluate side-chains 33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.092960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075291 restraints weight = 16109.046| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.76 r_work: 0.3023 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2562 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= 0.168 Angle : 0.491 6.190 4760 Z= 0.262 Chirality : 0.035 0.127 573 Planarity : 0.004 0.037 563 Dihedral : 6.048 56.092 666 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.40 % Allowed : 13.73 % Favored : 84.87 % 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: 2.86 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.21 (0.72), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.013 0.001 PHE A 114 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 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.490 Fit side-chains REVERT: A 171 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7228 (mpt90) REVERT: A 421 ASP cc_start: 0.8507 (p0) cc_final: 0.8256 (p0) REVERT: A 448 GLU cc_start: 0.8535 (tt0) cc_final: 0.8259 (tt0) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 1.9422 time to fit residues: 65.2828 Evaluate side-chains 33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.091945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.074342 restraints weight = 16372.860| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.77 r_work: 0.3012 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2573 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= 0.208 Angle : 0.507 6.232 4760 Z= 0.269 Chirality : 0.035 0.129 573 Planarity : 0.004 0.037 563 Dihedral : 6.110 56.830 666 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 14.01 % 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: 3.41 (0.40), residues: 420 helix: 2.88 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.32 (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 0.016 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 ********************** 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 to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.476 Fit side-chains REVERT: A 171 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7326 (mpt90) REVERT: A 421 ASP cc_start: 0.8537 (p0) cc_final: 0.8316 (p0) REVERT: A 448 GLU cc_start: 0.8540 (tt0) cc_final: 0.8275 (tt0) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 1.8121 time to fit residues: 60.8356 Evaluate side-chains 33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.092983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075462 restraints weight = 16207.315| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.76 r_work: 0.3029 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2571 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= 0.166 Angle : 0.494 6.159 4760 Z= 0.261 Chirality : 0.035 0.126 573 Planarity : 0.004 0.038 563 Dihedral : 6.023 56.314 666 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.12 % Allowed : 14.57 % 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: 3.45 (0.41), residues: 420 helix: 2.88 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.26 (0.72), 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 0.013 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: 5508.86 seconds wall clock time: 94 minutes 6.20 seconds (5646.20 seconds total)