Starting phenix.real_space_refine on Tue Jan 14 08:33:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.map" model { file = "/net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0r_43712/01_2025/8w0r_43712.cif" } resolution = 2.8 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= 0.009 sd= 0.257 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3400 atoms to isotropic. 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 12 5.16 5 C 2388 2.51 5 N 576 2.21 5 O 574 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1751 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1751 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A1AEU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A1AEU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.78 Number of scatterers: 3556 At special positions: 0 Unit cell: (74.4, 66, 78, 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 12 16.00 F 6 9.00 O 574 8.00 N 576 7.00 C 2388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.22 Conformation dependent library (CDL) restraints added in 420.5 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.831A pdb=" N ILE A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 87 removed outlier: 4.056A pdb=" N GLU A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 146 through 172 Processing helix chain 'A' and resid 190 through 219 removed outlier: 4.824A pdb=" N TRP A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.830A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 87 removed outlier: 4.055A pdb=" N GLU B 80 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 146 through 172 Processing helix chain 'B' and resid 190 through 219 removed outlier: 4.823A pdb=" N TRP B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 197 " --> pdb=" O ASN B 193 " (cutoff:3.500A) Proline residue: B 200 - end of helix 238 hydrogen bonds defined for protein. 714 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: 0.91 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1046 1.34 - 1.46: 734 1.46 - 1.57: 1896 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3692 Sorted by residual: bond pdb=" C07 A1AEU B 301 " pdb=" N01 A1AEU B 301 " ideal model delta sigma weight residual 1.451 1.515 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C07 A1AEU A 301 " pdb=" N01 A1AEU A 301 " ideal model delta sigma weight residual 1.451 1.514 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C04 A1AEU A 301 " pdb=" N01 A1AEU A 301 " ideal model delta sigma weight residual 1.451 1.509 -0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C04 A1AEU B 301 " pdb=" N01 A1AEU B 301 " ideal model delta sigma weight residual 1.451 1.509 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" C05 A1AEU A 301 " pdb=" N01 A1AEU A 301 " ideal model delta sigma weight residual 1.451 1.501 -0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 3687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 4977 2.06 - 4.13: 76 4.13 - 6.19: 13 6.19 - 8.26: 0 8.26 - 10.32: 4 Bond angle restraints: 5070 Sorted by residual: angle pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " pdb=" CD2 LEU A 197 " ideal model delta sigma weight residual 110.70 121.02 -10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB LEU B 197 " pdb=" CG LEU B 197 " pdb=" CD2 LEU B 197 " ideal model delta sigma weight residual 110.70 121.00 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " pdb=" CD1 LEU A 197 " ideal model delta sigma weight residual 110.70 119.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" CB LEU B 197 " pdb=" CG LEU B 197 " pdb=" CD1 LEU B 197 " ideal model delta sigma weight residual 110.70 119.48 -8.78 3.00e+00 1.11e-01 8.56e+00 angle pdb=" CD1 LEU B 197 " pdb=" CG LEU B 197 " pdb=" CD2 LEU B 197 " ideal model delta sigma weight residual 110.80 116.87 -6.07 2.20e+00 2.07e-01 7.62e+00 ... (remaining 5065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.15: 1722 11.15 - 22.29: 276 22.29 - 33.44: 80 33.44 - 44.58: 16 44.58 - 55.73: 8 Dihedral angle restraints: 2102 sinusoidal: 872 harmonic: 1230 Sorted by residual: dihedral pdb=" CA HIS A 144 " pdb=" C HIS A 144 " pdb=" N PRO A 145 " pdb=" CA PRO A 145 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA HIS B 144 " pdb=" C HIS B 144 " pdb=" N PRO B 145 " pdb=" CA PRO B 145 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TRP A 196 " pdb=" C TRP A 196 " pdb=" N LEU A 197 " pdb=" CA LEU A 197 " ideal model delta harmonic sigma weight residual 180.00 163.91 16.09 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 548 0.339 - 0.677: 0 0.677 - 1.016: 0 1.016 - 1.354: 0 1.354 - 1.692: 2 Chirality restraints: 550 Sorted by residual: chirality pdb=" CG LEU A 197 " pdb=" CB LEU A 197 " pdb=" CD1 LEU A 197 " pdb=" CD2 LEU A 197 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.16e+01 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CA VAL A 22 " pdb=" N VAL A 22 " pdb=" C VAL A 22 " pdb=" CB VAL A 22 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 547 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 144 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO B 145 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 144 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 145 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 52 " -0.123 9.50e-02 1.11e+02 5.55e-02 2.04e+00 pdb=" NE ARG A 52 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 52 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 52 " -0.002 2.00e-02 2.50e+03 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 16 2.64 - 3.20: 3270 3.20 - 3.77: 5582 3.77 - 4.33: 7661 4.33 - 4.90: 12858 Nonbonded interactions: 29387 Sorted by model distance: nonbonded pdb=" OD2 ASP A 108 " pdb=" OH TYR A 165 " model vdw 2.073 3.040 nonbonded pdb=" OD2 ASP B 108 " pdb=" OH TYR B 165 " model vdw 2.073 3.040 nonbonded pdb=" OH TYR B 11 " pdb=" O LYS B 102 " model vdw 2.355 3.040 nonbonded pdb=" OH TYR A 11 " pdb=" O LYS A 102 " model vdw 2.356 3.040 nonbonded pdb=" O TRP A 129 " pdb=" OG SER A 133 " model vdw 2.472 3.040 ... (remaining 29382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.070 Find NCS groups from input model: 0.060 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.005 0.064 3692 Z= 0.294 Angle : 0.713 10.320 5070 Z= 0.349 Chirality : 0.109 1.692 550 Planarity : 0.006 0.055 610 Dihedral : 12.169 55.727 1314 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.55 (0.43), residues: 422 helix: 0.44 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.61 (0.74), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 29 HIS 0.003 0.001 HIS A 76 PHE 0.009 0.001 PHE B 189 TYR 0.019 0.002 TYR B 86 ARG 0.007 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.7836 time to fit residues: 60.5060 Evaluate side-chains 31 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 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 = 0.3781 r_free = 0.3781 target = 0.160667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150725 restraints weight = 3949.399| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.06 r_work: 0.3619 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3692 Z= 0.162 Angle : 0.506 6.136 5070 Z= 0.268 Chirality : 0.040 0.143 550 Planarity : 0.005 0.039 610 Dihedral : 4.767 16.556 560 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.71 (0.42), residues: 422 helix: 1.27 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 1.00 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.002 0.001 HIS A 30 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.002 TYR A 86 ARG 0.006 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.364 Fit side-chains REVERT: A 50 SER cc_start: 0.7908 (m) cc_final: 0.7390 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 1.7516 time to fit residues: 57.6115 Evaluate side-chains 29 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.157588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147722 restraints weight = 4080.934| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.13 r_work: 0.3620 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3692 Z= 0.188 Angle : 0.508 5.908 5070 Z= 0.264 Chirality : 0.040 0.144 550 Planarity : 0.005 0.037 610 Dihedral : 4.519 15.043 560 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.27 % Allowed : 7.53 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.42), residues: 422 helix: 1.57 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.93 (0.70), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.003 0.001 HIS A 15 PHE 0.007 0.001 PHE A 189 TYR 0.020 0.002 TYR A 86 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.387 Fit side-chains REVERT: A 50 SER cc_start: 0.7945 (m) cc_final: 0.7510 (t) REVERT: B 50 SER cc_start: 0.7935 (m) cc_final: 0.7535 (t) REVERT: B 143 GLN cc_start: 0.8140 (mt0) cc_final: 0.7888 (mt0) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 1.6143 time to fit residues: 58.2706 Evaluate side-chains 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.151859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141933 restraints weight = 4179.049| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.15 r_work: 0.3551 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3692 Z= 0.313 Angle : 0.604 7.449 5070 Z= 0.308 Chirality : 0.043 0.146 550 Planarity : 0.005 0.037 610 Dihedral : 4.911 14.885 560 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.99 (0.42), residues: 422 helix: 1.58 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.69 (0.68), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 29 HIS 0.004 0.002 HIS A 76 PHE 0.010 0.002 PHE A 117 TYR 0.025 0.002 TYR B 86 ARG 0.003 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.403 Fit side-chains REVERT: A 50 SER cc_start: 0.8017 (m) cc_final: 0.7656 (t) REVERT: A 143 GLN cc_start: 0.8162 (mt0) cc_final: 0.7925 (mt0) REVERT: B 50 SER cc_start: 0.8054 (m) cc_final: 0.7709 (t) REVERT: B 143 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (mt0) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 1.5736 time to fit residues: 55.1814 Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 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 = 0.3766 r_free = 0.3766 target = 0.158231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148357 restraints weight = 4156.475| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.17 r_work: 0.3609 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3692 Z= 0.166 Angle : 0.472 4.870 5070 Z= 0.246 Chirality : 0.038 0.131 550 Planarity : 0.004 0.035 610 Dihedral : 4.338 15.156 560 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.42), residues: 422 helix: 1.66 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.83 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.002 0.001 HIS A 15 PHE 0.006 0.001 PHE B 191 TYR 0.021 0.002 TYR A 86 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.388 Fit side-chains REVERT: A 50 SER cc_start: 0.8005 (m) cc_final: 0.7639 (t) REVERT: B 50 SER cc_start: 0.8032 (m) cc_final: 0.7677 (t) REVERT: B 143 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (mt0) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 1.2743 time to fit residues: 46.2594 Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.155940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146104 restraints weight = 4225.526| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.16 r_work: 0.3545 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3692 Z= 0.204 Angle : 0.499 4.830 5070 Z= 0.261 Chirality : 0.039 0.138 550 Planarity : 0.004 0.035 610 Dihedral : 4.362 14.917 560 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.81 % Allowed : 11.56 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.42), residues: 422 helix: 1.65 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.82 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.003 0.001 HIS B 15 PHE 0.006 0.001 PHE A 117 TYR 0.024 0.002 TYR A 86 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.365 Fit side-chains REVERT: A 50 SER cc_start: 0.7964 (m) cc_final: 0.7627 (t) REVERT: B 50 SER cc_start: 0.7984 (m) cc_final: 0.7694 (t) REVERT: B 143 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7979 (mt0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 1.2440 time to fit residues: 47.7787 Evaluate side-chains 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.157852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148197 restraints weight = 4064.605| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.14 r_work: 0.3605 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3692 Z= 0.164 Angle : 0.467 4.104 5070 Z= 0.247 Chirality : 0.038 0.134 550 Planarity : 0.004 0.034 610 Dihedral : 4.145 15.021 560 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.61 % Allowed : 11.02 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.41), residues: 422 helix: 1.78 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.88 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.002 0.001 HIS B 15 PHE 0.009 0.001 PHE A 185 TYR 0.012 0.001 TYR B 165 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.418 Fit side-chains REVERT: A 50 SER cc_start: 0.7958 (m) cc_final: 0.7618 (t) REVERT: A 143 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: B 50 SER cc_start: 0.7955 (m) cc_final: 0.7674 (t) REVERT: B 143 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7973 (mt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.1404 time to fit residues: 44.0574 Evaluate side-chains 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.156343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146609 restraints weight = 4154.982| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.16 r_work: 0.3551 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3692 Z= 0.201 Angle : 0.491 4.292 5070 Z= 0.259 Chirality : 0.039 0.133 550 Planarity : 0.004 0.034 610 Dihedral : 4.223 14.933 560 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.02 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.41), residues: 422 helix: 1.73 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.78 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.002 0.001 HIS B 15 PHE 0.012 0.001 PHE B 185 TYR 0.012 0.001 TYR A 165 ARG 0.003 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.393 Fit side-chains REVERT: A 50 SER cc_start: 0.7982 (m) cc_final: 0.7646 (t) REVERT: A 143 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: B 50 SER cc_start: 0.7953 (m) cc_final: 0.7672 (t) REVERT: B 143 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (mt0) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 1.2593 time to fit residues: 47.0255 Evaluate side-chains 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 19 optimal weight: 0.1980 overall best weight: 1.6444 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.150411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140728 restraints weight = 4166.917| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.12 r_work: 0.3512 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3692 Z= 0.318 Angle : 0.588 5.367 5070 Z= 0.304 Chirality : 0.043 0.139 550 Planarity : 0.005 0.034 610 Dihedral : 4.663 14.871 560 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.02 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 422 helix: 1.62 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.64 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 61 HIS 0.004 0.002 HIS A 30 PHE 0.016 0.002 PHE B 185 TYR 0.012 0.002 TYR B 165 ARG 0.003 0.001 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.370 Fit side-chains REVERT: A 50 SER cc_start: 0.8020 (m) cc_final: 0.7686 (t) REVERT: A 143 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: B 50 SER cc_start: 0.7985 (m) cc_final: 0.7695 (t) REVERT: B 143 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8033 (mt0) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 1.1592 time to fit residues: 44.6480 Evaluate side-chains 38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 32 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 = 0.3739 r_free = 0.3739 target = 0.155999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146373 restraints weight = 4155.491| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.15 r_work: 0.3539 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3692 Z= 0.204 Angle : 0.504 4.536 5070 Z= 0.266 Chirality : 0.039 0.134 550 Planarity : 0.004 0.034 610 Dihedral : 4.319 15.025 560 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 11.29 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.41), residues: 422 helix: 1.65 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.68 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.002 0.001 HIS B 15 PHE 0.014 0.001 PHE B 185 TYR 0.012 0.001 TYR B 165 ARG 0.004 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.366 Fit side-chains REVERT: A 50 SER cc_start: 0.7997 (m) cc_final: 0.7652 (t) REVERT: A 143 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: B 50 SER cc_start: 0.7965 (m) cc_final: 0.7670 (t) REVERT: B 143 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7977 (mt0) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 1.0562 time to fit residues: 38.6077 Evaluate side-chains 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.155495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145975 restraints weight = 4136.630| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.11 r_work: 0.3555 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3692 Z= 0.187 Angle : 0.488 4.131 5070 Z= 0.259 Chirality : 0.039 0.131 550 Planarity : 0.004 0.033 610 Dihedral : 4.205 14.859 560 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 11.83 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.41), residues: 422 helix: 1.74 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.74 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.014 0.001 PHE B 185 TYR 0.012 0.001 TYR B 165 ARG 0.004 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2326.40 seconds wall clock time: 41 minutes 58.80 seconds (2518.80 seconds total)