Starting phenix.real_space_refine on Sun Apr 27 17:00:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0r_43712/04_2025/8w0r_43712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0r_43712/04_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_43712/04_2025/8w0r_43712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0r_43712/04_2025/8w0r_43712.map" model { file = "/net/cci-nas-00/data/ceres_data/8w0r_43712/04_2025/8w0r_43712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0r_43712/04_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-5669/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: 3.06, per 1000 atoms: 0.86 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: 0.98 Conformation dependent library (CDL) restraints added in 406.6 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: 0.36 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: 0.88 Time building geometry restraints manager: 1.12 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: 0.410 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- 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= 0.214 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 Details of bonding type rmsd hydrogen bonds : bond 0.14526 ( 238) hydrogen bonds : angle 6.45065 ( 714) covalent geometry : bond 0.00479 ( 3692) covalent geometry : angle 0.71279 ( 5070) *********************** 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 : 0.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.7206 time to fit residues: 58.3267 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 : 0.364 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150726 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: 3.16 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= 0.122 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 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 238) hydrogen bonds : angle 4.08526 ( 714) covalent geometry : bond 0.00268 ( 3692) covalent geometry : angle 0.50566 ( 5070) *********************** 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 : 0.335 Fit side-chains REVERT: A 50 SER cc_start: 0.7907 (m) cc_final: 0.7389 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 1.7856 time to fit residues: 58.7411 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 : 0.337 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.157761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148032 restraints weight = 4080.008| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.09 r_work: 0.3636 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1770 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= 0.128 Angle : 0.497 5.613 5070 Z= 0.259 Chirality : 0.039 0.144 550 Planarity : 0.004 0.037 610 Dihedral : 4.474 15.090 560 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.27 % Allowed : 6.72 % Favored : 93.01 % 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 (0.42), residues: 422 helix: 1.59 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.94 (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 B 189 TYR 0.019 0.002 TYR A 86 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 238) hydrogen bonds : angle 3.87613 ( 714) covalent geometry : bond 0.00292 ( 3692) covalent geometry : angle 0.49726 ( 5070) *********************** 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 : 0.441 Fit side-chains REVERT: A 50 SER cc_start: 0.7937 (m) cc_final: 0.7499 (t) REVERT: B 50 SER cc_start: 0.7927 (m) cc_final: 0.7525 (t) REVERT: B 143 GLN cc_start: 0.8131 (mt0) cc_final: 0.7874 (mt0) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 2.0076 time to fit residues: 72.4780 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 : 0.422 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 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: 0.0020 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.150397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140606 restraints weight = 4199.629| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.12 r_work: 0.3494 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3692 Z= 0.245 Angle : 0.648 8.355 5070 Z= 0.328 Chirality : 0.045 0.147 550 Planarity : 0.005 0.037 610 Dihedral : 5.066 15.239 560 Min Nonbonded Distance : 2.618 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: 1.80 (0.42), residues: 422 helix: 1.44 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.65 (0.67), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 29 HIS 0.005 0.002 HIS B 15 PHE 0.011 0.002 PHE A 117 TYR 0.024 0.002 TYR A 86 ARG 0.003 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05746 ( 238) hydrogen bonds : angle 4.17856 ( 714) covalent geometry : bond 0.00587 ( 3692) covalent geometry : angle 0.64823 ( 5070) *********************** 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 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.392 Fit side-chains REVERT: A 50 SER cc_start: 0.8021 (m) cc_final: 0.7670 (t) REVERT: A 143 GLN cc_start: 0.8227 (mt0) cc_final: 0.7967 (mt0) REVERT: B 50 SER cc_start: 0.8061 (m) cc_final: 0.7706 (t) REVERT: B 143 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7935 (mt0) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 2.7174 time to fit residues: 97.4129 Evaluate side-chains 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.155209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145370 restraints weight = 4178.100| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.16 r_work: 0.3554 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2142 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= 0.126 Angle : 0.488 4.982 5070 Z= 0.254 Chirality : 0.039 0.133 550 Planarity : 0.004 0.035 610 Dihedral : 4.465 15.103 560 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.81 % Allowed : 10.22 % Favored : 88.98 % 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: 2.04 (0.42), residues: 422 helix: 1.58 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.76 (0.68), 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 15 PHE 0.006 0.001 PHE B 191 TYR 0.021 0.002 TYR A 86 ARG 0.006 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 238) hydrogen bonds : angle 3.86312 ( 714) covalent geometry : bond 0.00291 ( 3692) covalent geometry : angle 0.48767 ( 5070) *********************** 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 39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.394 Fit side-chains REVERT: A 50 SER cc_start: 0.7997 (m) cc_final: 0.7628 (t) REVERT: A 143 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: B 50 SER cc_start: 0.8024 (m) cc_final: 0.7672 (t) REVERT: B 143 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7953 (mt0) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 1.2021 time to fit residues: 47.4060 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 37 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 = 0.3744 r_free = 0.3744 target = 0.156354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146429 restraints weight = 4209.819| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.16 r_work: 0.3582 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2264 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= 0.114 Angle : 0.460 4.251 5070 Z= 0.242 Chirality : 0.038 0.133 550 Planarity : 0.004 0.034 610 Dihedral : 4.163 15.064 560 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.08 % Allowed : 11.29 % 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: 2.31 (0.42), residues: 422 helix: 1.78 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.85 (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 30 PHE 0.005 0.001 PHE A 117 TYR 0.023 0.002 TYR A 86 ARG 0.001 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 238) hydrogen bonds : angle 3.72768 ( 714) covalent geometry : bond 0.00261 ( 3692) covalent geometry : angle 0.45967 ( 5070) *********************** 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: 4 poor density : 33 time to evaluate : 0.346 Fit side-chains REVERT: A 50 SER cc_start: 0.7954 (m) cc_final: 0.7614 (t) REVERT: A 143 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: B 50 SER cc_start: 0.7952 (m) cc_final: 0.7673 (t) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 1.3772 time to fit residues: 51.3160 Evaluate side-chains 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.157275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147645 restraints weight = 4077.857| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.13 r_work: 0.3569 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2304 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= 0.122 Angle : 0.469 4.315 5070 Z= 0.248 Chirality : 0.038 0.133 550 Planarity : 0.004 0.034 610 Dihedral : 4.157 15.015 560 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.61 % Allowed : 10.75 % 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: 2.31 (0.42), residues: 422 helix: 1.78 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.87 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.010 0.001 PHE B 185 TYR 0.011 0.001 TYR A 165 ARG 0.001 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 238) hydrogen bonds : angle 3.75051 ( 714) covalent geometry : bond 0.00283 ( 3692) covalent geometry : angle 0.46909 ( 5070) *********************** 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 : 0.367 Fit side-chains REVERT: A 50 SER cc_start: 0.7960 (m) cc_final: 0.7628 (t) REVERT: B 50 SER cc_start: 0.7886 (m) cc_final: 0.7595 (t) REVERT: B 143 GLN cc_start: 0.7805 (mt0) cc_final: 0.7449 (mt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.0855 time to fit residues: 41.8358 Evaluate side-chains 32 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 49 LEU 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.153468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143698 restraints weight = 4189.880| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.15 r_work: 0.3521 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3692 Z= 0.170 Angle : 0.535 5.050 5070 Z= 0.278 Chirality : 0.041 0.138 550 Planarity : 0.004 0.034 610 Dihedral : 4.435 14.909 560 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.81 % Allowed : 11.02 % Favored : 88.17 % 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: 2.22 (0.41), residues: 422 helix: 1.75 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.77 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.003 0.001 HIS A 15 PHE 0.013 0.001 PHE B 185 TYR 0.027 0.002 TYR A 86 ARG 0.002 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 238) hydrogen bonds : angle 3.89054 ( 714) covalent geometry : bond 0.00407 ( 3692) covalent geometry : angle 0.53470 ( 5070) *********************** 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: 3 poor density : 35 time to evaluate : 0.350 Fit side-chains REVERT: A 50 SER cc_start: 0.7995 (m) cc_final: 0.7664 (t) REVERT: A 143 GLN cc_start: 0.8003 (mt0) cc_final: 0.7694 (mt0) REVERT: B 50 SER cc_start: 0.7967 (m) cc_final: 0.7670 (t) REVERT: B 143 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7433 (mt0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 2.0739 time to fit residues: 78.5886 Evaluate side-chains 38 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 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 = 0.3730 r_free = 0.3730 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145690 restraints weight = 4119.226| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.12 r_work: 0.3545 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2367 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= 0.136 Angle : 0.492 4.456 5070 Z= 0.257 Chirality : 0.039 0.132 550 Planarity : 0.004 0.034 610 Dihedral : 4.267 15.022 560 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.34 % Allowed : 10.75 % Favored : 87.90 % 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: 2.18 (0.41), residues: 422 helix: 1.70 (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 0.013 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.013 0.001 PHE B 185 TYR 0.012 0.001 TYR A 165 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 238) hydrogen bonds : angle 3.82033 ( 714) covalent geometry : bond 0.00321 ( 3692) covalent geometry : angle 0.49249 ( 5070) *********************** 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 37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.419 Fit side-chains REVERT: A 50 SER cc_start: 0.7984 (m) cc_final: 0.7646 (t) REVERT: A 143 GLN cc_start: 0.7920 (mt0) cc_final: 0.7617 (mt0) REVERT: B 50 SER cc_start: 0.7953 (m) cc_final: 0.7655 (t) REVERT: B 143 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7406 (mt0) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 2.5010 time to fit residues: 89.6116 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 142 ARG 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: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.153733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144135 restraints weight = 4171.703| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.13 r_work: 0.3529 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3692 Z= 0.159 Angle : 0.526 4.582 5070 Z= 0.276 Chirality : 0.040 0.133 550 Planarity : 0.004 0.034 610 Dihedral : 4.357 14.929 560 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.85 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: 2.25 (0.41), residues: 422 helix: 1.78 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.73 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 29 HIS 0.003 0.001 HIS B 15 PHE 0.015 0.001 PHE B 185 TYR 0.012 0.001 TYR A 165 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 238) hydrogen bonds : angle 3.85760 ( 714) covalent geometry : bond 0.00378 ( 3692) covalent geometry : angle 0.52608 ( 5070) ********************** 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 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.408 Fit side-chains REVERT: A 50 SER cc_start: 0.7992 (m) cc_final: 0.7659 (t) REVERT: A 143 GLN cc_start: 0.7971 (mt0) cc_final: 0.7671 (mt0) REVERT: B 50 SER cc_start: 0.7960 (m) cc_final: 0.7667 (t) REVERT: B 143 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7446 (mt0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 1.2124 time to fit residues: 45.3572 Evaluate side-chains 36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.155819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146316 restraints weight = 4132.177| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.10 r_work: 0.3577 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2410 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= 0.118 Angle : 0.469 4.039 5070 Z= 0.248 Chirality : 0.038 0.129 550 Planarity : 0.004 0.034 610 Dihedral : 4.098 14.977 560 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 5.71 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: 2.36 (0.41), residues: 422 helix: 1.83 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.80 (0.66), 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 0.013 0.001 PHE B 185 TYR 0.012 0.001 TYR B 165 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 238) hydrogen bonds : angle 3.74218 ( 714) covalent geometry : bond 0.00273 ( 3692) covalent geometry : angle 0.46866 ( 5070) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2883.58 seconds wall clock time: 52 minutes 29.36 seconds (3149.36 seconds total)