Starting phenix.real_space_refine on Sat May 10 21:16:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc0_42111/05_2025/8uc0_42111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc0_42111/05_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_42111/05_2025/8uc0_42111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc0_42111/05_2025/8uc0_42111.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc0_42111/05_2025/8uc0_42111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc0_42111/05_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-5687/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: 4.63, per 1000 atoms: 0.67 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: 1.95 Conformation dependent library (CDL) restraints added in 618.1 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: 0.41 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: 2.36 Time building geometry restraints manager: 2.32 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: 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: 3.180 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.810 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- 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= 0.110 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 Details of bonding type rmsd hydrogen bonds : bond 0.12218 ( 279) hydrogen bonds : angle 5.92053 ( 837) covalent geometry : bond 0.00205 ( 3477) covalent geometry : angle 0.47353 ( 4760) *********************** 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 : 0.485 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 2.1490 time to fit residues: 102.5516 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 : 0.524 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078749 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: 0.2957 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 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= 0.176 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 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 279) hydrogen bonds : angle 4.58318 ( 837) covalent geometry : bond 0.00385 ( 3477) covalent geometry : angle 0.54292 ( 4760) *********************** 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 : 0.534 Fit side-chains REVERT: A 171 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7496 (mpt90) REVERT: A 312 GLN cc_start: 0.6961 (mt0) cc_final: 0.6697 (mt0) REVERT: A 421 ASP cc_start: 0.8521 (p0) cc_final: 0.8233 (p0) REVERT: A 448 GLU cc_start: 0.8482 (tt0) cc_final: 0.8140 (tt0) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 2.0453 time to fit residues: 85.2407 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 : 0.484 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.093393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075562 restraints weight = 16060.495| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.78 r_work: 0.3027 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3477 Z= 0.161 Angle : 0.510 6.202 4760 Z= 0.274 Chirality : 0.035 0.129 573 Planarity : 0.004 0.037 563 Dihedral : 6.004 53.369 666 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.68 % Allowed : 12.32 % 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: 2.90 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -0.88 (0.82), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.016 0.001 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 279) hydrogen bonds : angle 4.49112 ( 837) covalent geometry : bond 0.00351 ( 3477) covalent geometry : angle 0.50959 ( 4760) *********************** 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 40 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.524 Fit side-chains REVERT: A 171 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7277 (mpt90) REVERT: A 312 GLN cc_start: 0.6932 (mt0) cc_final: 0.6684 (mt0) REVERT: A 448 GLU cc_start: 0.8551 (tt0) cc_final: 0.8214 (tt0) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 1.9890 time to fit residues: 76.7641 Evaluate side-chains 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 26 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 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 = 0.3313 r_free = 0.3313 target = 0.094159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076348 restraints weight = 16319.984| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.78 r_work: 0.3042 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2120 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= 0.130 Angle : 0.490 6.102 4760 Z= 0.262 Chirality : 0.034 0.127 573 Planarity : 0.004 0.037 563 Dihedral : 5.863 55.932 666 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.59 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: 3.56 (0.41), residues: 420 helix: 2.92 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.04 (0.79), 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 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 279) hydrogen bonds : angle 4.32615 ( 837) covalent geometry : bond 0.00272 ( 3477) covalent geometry : angle 0.48953 ( 4760) *********************** 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 : 0.468 Fit side-chains REVERT: A 171 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7303 (mpt90) REVERT: A 312 GLN cc_start: 0.6932 (mt0) cc_final: 0.6731 (mt0) REVERT: A 421 ASP cc_start: 0.8486 (p0) cc_final: 0.8112 (p0) REVERT: A 448 GLU cc_start: 0.8551 (tt0) cc_final: 0.8280 (tt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 2.1195 time to fit residues: 77.2491 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 : 0.552 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.092473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074773 restraints weight = 16053.793| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.76 r_work: 0.3012 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2293 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= 0.156 Angle : 0.503 6.155 4760 Z= 0.270 Chirality : 0.035 0.131 573 Planarity : 0.004 0.037 563 Dihedral : 6.079 59.811 666 Min Nonbonded Distance : 2.456 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: 3.50 (0.41), residues: 420 helix: 2.91 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.10 (0.75), 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 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 279) hydrogen bonds : angle 4.36438 ( 837) covalent geometry : bond 0.00343 ( 3477) covalent geometry : angle 0.50254 ( 4760) *********************** 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 : 0.488 Fit side-chains REVERT: A 171 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7304 (mpt90) REVERT: A 421 ASP cc_start: 0.8543 (p0) cc_final: 0.8277 (p0) REVERT: A 448 GLU cc_start: 0.8576 (tt0) cc_final: 0.8308 (tt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 2.1093 time to fit residues: 76.8220 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 : 0.534 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074818 restraints weight = 16162.489| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.77 r_work: 0.3013 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2368 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= 0.146 Angle : 0.495 6.178 4760 Z= 0.266 Chirality : 0.035 0.131 573 Planarity : 0.004 0.037 563 Dihedral : 6.058 57.996 666 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 12.89 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.41), residues: 420 helix: 2.91 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.16 (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 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 279) hydrogen bonds : angle 4.33180 ( 837) covalent geometry : bond 0.00316 ( 3477) covalent geometry : angle 0.49538 ( 4760) *********************** 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 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.512 Fit side-chains REVERT: A 171 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7280 (mpt90) REVERT: A 421 ASP cc_start: 0.8557 (p0) cc_final: 0.8262 (p0) REVERT: A 448 GLU cc_start: 0.8575 (tt0) cc_final: 0.8305 (tt0) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 2.1312 time to fit residues: 73.2725 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 : 0.489 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075839 restraints weight = 15941.465| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.75 r_work: 0.3031 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3477 Z= 0.125 Angle : 0.484 6.128 4760 Z= 0.259 Chirality : 0.034 0.127 573 Planarity : 0.004 0.037 563 Dihedral : 5.956 57.677 666 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.12 % Allowed : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.41), residues: 420 helix: 2.91 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.12 (0.75), 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 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 279) hydrogen bonds : angle 4.26935 ( 837) covalent geometry : bond 0.00257 ( 3477) covalent geometry : angle 0.48382 ( 4760) *********************** 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 to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.483 Fit side-chains REVERT: A 171 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7245 (mpt90) REVERT: A 421 ASP cc_start: 0.8536 (p0) cc_final: 0.8189 (p0) REVERT: A 448 GLU cc_start: 0.8553 (tt0) cc_final: 0.8294 (tt0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 2.3155 time to fit residues: 77.2019 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 : 0.532 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 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 = 0.3281 r_free = 0.3281 target = 0.092174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.074470 restraints weight = 16181.190| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.77 r_work: 0.3007 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2509 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= 0.152 Angle : 0.500 6.205 4760 Z= 0.268 Chirality : 0.035 0.130 573 Planarity : 0.004 0.038 563 Dihedral : 6.065 56.638 666 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 : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.41), residues: 420 helix: 2.92 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.26 (0.70), 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 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 279) hydrogen bonds : angle 4.32577 ( 837) covalent geometry : bond 0.00334 ( 3477) covalent geometry : angle 0.49978 ( 4760) *********************** 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 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.500 Fit side-chains REVERT: A 171 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7268 (mpt90) REVERT: A 448 GLU cc_start: 0.8555 (tt0) cc_final: 0.8297 (tt0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 1.9503 time to fit residues: 65.3662 Evaluate side-chains 32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 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: 0.9980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075578 restraints weight = 16095.457| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.77 r_work: 0.3023 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 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 0.021 3477 Z= 0.126 Angle : 0.488 6.145 4760 Z= 0.260 Chirality : 0.035 0.127 573 Planarity : 0.004 0.038 563 Dihedral : 5.987 56.126 666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.12 % Allowed : 14.01 % 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: 3.50 (0.41), residues: 420 helix: 2.90 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.18 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.014 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 279) hydrogen bonds : angle 4.26070 ( 837) covalent geometry : bond 0.00262 ( 3477) covalent geometry : angle 0.48842 ( 4760) *********************** 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: 4 poor density : 30 time to evaluate : 0.520 Fit side-chains REVERT: A 171 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7137 (mpt90) REVERT: A 421 ASP cc_start: 0.8493 (p0) cc_final: 0.8214 (p0) REVERT: A 448 GLU cc_start: 0.8541 (tt0) cc_final: 0.8270 (tt0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 1.9183 time to fit residues: 64.2508 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 : 0.518 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074908 restraints weight = 16386.924| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.77 r_work: 0.3010 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2531 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= 0.147 Angle : 0.501 6.179 4760 Z= 0.267 Chirality : 0.035 0.128 573 Planarity : 0.004 0.038 563 Dihedral : 6.039 56.562 666 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.03 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: 3.47 (0.40), residues: 420 helix: 2.92 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.28 (0.70), 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 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 279) hydrogen bonds : angle 4.29558 ( 837) covalent geometry : bond 0.00323 ( 3477) covalent geometry : angle 0.50096 ( 4760) ********************** 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 : 0.554 Fit side-chains REVERT: A 171 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7258 (mpt90) REVERT: A 421 ASP cc_start: 0.8499 (p0) cc_final: 0.8226 (p0) REVERT: A 448 GLU cc_start: 0.8546 (tt0) cc_final: 0.8275 (tt0) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 1.8965 time to fit residues: 63.7975 Evaluate side-chains 32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.092775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075167 restraints weight = 16275.697| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.77 r_work: 0.3018 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2555 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= 0.138 Angle : 0.502 6.176 4760 Z= 0.265 Chirality : 0.035 0.128 573 Planarity : 0.004 0.038 563 Dihedral : 6.033 56.588 666 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.84 % Allowed : 14.57 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.41), residues: 420 helix: 2.92 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.28 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 279) hydrogen bonds : angle 4.28005 ( 837) covalent geometry : bond 0.00297 ( 3477) covalent geometry : angle 0.50168 ( 4760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5082.97 seconds wall clock time: 87 minutes 46.37 seconds (5266.37 seconds total)