Starting phenix.real_space_refine on Wed Sep 17 06:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0r_43712/09_2025/8w0r_43712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0r_43712/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w0r_43712/09_2025/8w0r_43712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0r_43712/09_2025/8w0r_43712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w0r_43712/09_2025/8w0r_43712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0r_43712/09_2025/8w0r_43712.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.28 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: 0.26 Conformation dependent library (CDL) restraints added in 137.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.54 Time building geometry restraints manager: 0.34 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: 0.01 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.010 Find NCS groups from input model: 0.030 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A 52 TYR 0.019 0.002 TYR B 86 PHE 0.009 0.001 PHE B 189 TRP 0.018 0.001 TRP A 29 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 3692) covalent geometry : angle 0.71279 ( 5070) hydrogen bonds : bond 0.14526 ( 238) hydrogen bonds : angle 6.45065 ( 714) *********************** 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 : 0.129 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.9731 time to fit residues: 32.8168 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 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 = 0.3761 r_free = 0.3761 target = 0.158809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148603 restraints weight = 4094.690| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.10 r_work: 0.3598 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1295 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= 0.128 Angle : 0.514 6.397 5070 Z= 0.272 Chirality : 0.040 0.137 550 Planarity : 0.005 0.039 610 Dihedral : 4.858 16.830 560 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.42), residues: 422 helix: 1.22 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.97 (0.72), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 52 TYR 0.015 0.002 TYR B 86 PHE 0.010 0.001 PHE A 189 TRP 0.015 0.001 TRP A 29 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3692) covalent geometry : angle 0.51391 ( 5070) hydrogen bonds : bond 0.04584 ( 238) hydrogen bonds : angle 4.14069 ( 714) *********************** 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 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.138 Fit side-chains REVERT: A 50 SER cc_start: 0.7911 (m) cc_final: 0.7396 (t) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.9037 time to fit residues: 30.5361 Evaluate side-chains 30 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.157290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147304 restraints weight = 4133.987| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.15 r_work: 0.3572 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3692 Z= 0.136 Angle : 0.521 6.013 5070 Z= 0.267 Chirality : 0.040 0.142 550 Planarity : 0.005 0.037 610 Dihedral : 4.571 15.246 560 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.27 % Allowed : 8.33 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.42), residues: 422 helix: 1.56 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.88 (0.70), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 52 TYR 0.020 0.002 TYR B 86 PHE 0.007 0.001 PHE B 189 TRP 0.013 0.001 TRP A 29 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3692) covalent geometry : angle 0.52078 ( 5070) hydrogen bonds : bond 0.04510 ( 238) hydrogen bonds : angle 3.91999 ( 714) *********************** 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 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.129 Fit side-chains REVERT: A 50 SER cc_start: 0.7942 (m) cc_final: 0.7515 (t) REVERT: B 50 SER cc_start: 0.7951 (m) cc_final: 0.7555 (t) REVERT: B 143 GLN cc_start: 0.8152 (mt0) cc_final: 0.7902 (mt0) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.8237 time to fit residues: 28.7316 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 : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 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 = 0.3767 r_free = 0.3767 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148767 restraints weight = 4093.770| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.14 r_work: 0.3623 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2001 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= 0.120 Angle : 0.471 4.360 5070 Z= 0.247 Chirality : 0.039 0.138 550 Planarity : 0.004 0.035 610 Dihedral : 4.315 15.221 560 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.27 % Allowed : 9.68 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.42), residues: 422 helix: 1.73 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.89 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.022 0.002 TYR A 86 PHE 0.005 0.001 PHE B 117 TRP 0.014 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3692) covalent geometry : angle 0.47062 ( 5070) hydrogen bonds : bond 0.04048 ( 238) hydrogen bonds : angle 3.79244 ( 714) *********************** 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 34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.132 Fit side-chains REVERT: A 50 SER cc_start: 0.7945 (m) cc_final: 0.7530 (t) REVERT: B 50 SER cc_start: 0.7939 (m) cc_final: 0.7562 (t) REVERT: B 143 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (mt0) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.7527 time to fit residues: 26.3325 Evaluate side-chains 29 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.159810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150024 restraints weight = 4116.402| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.12 r_work: 0.3600 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3692 Z= 0.109 Angle : 0.449 4.051 5070 Z= 0.237 Chirality : 0.038 0.137 550 Planarity : 0.004 0.034 610 Dihedral : 4.119 15.225 560 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.27 % Allowed : 10.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.42), residues: 422 helix: 1.85 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 1.00 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.022 0.002 TYR A 86 PHE 0.005 0.001 PHE B 189 TRP 0.013 0.001 TRP A 29 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3692) covalent geometry : angle 0.44868 ( 5070) hydrogen bonds : bond 0.03822 ( 238) hydrogen bonds : angle 3.71002 ( 714) *********************** 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 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.142 Fit side-chains REVERT: A 50 SER cc_start: 0.7901 (m) cc_final: 0.7527 (t) REVERT: B 50 SER cc_start: 0.7885 (m) cc_final: 0.7577 (t) REVERT: B 143 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (mt0) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.6413 time to fit residues: 21.8709 Evaluate side-chains 31 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 3 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.155079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145197 restraints weight = 4168.582| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.17 r_work: 0.3588 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2249 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= 0.159 Angle : 0.513 4.907 5070 Z= 0.268 Chirality : 0.040 0.138 550 Planarity : 0.004 0.034 610 Dihedral : 4.408 14.894 560 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.54 % Allowed : 11.02 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.42), residues: 422 helix: 1.73 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 0.69 (0.69), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.024 0.002 TYR A 86 PHE 0.007 0.001 PHE A 117 TRP 0.010 0.001 TRP B 29 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3692) covalent geometry : angle 0.51318 ( 5070) hydrogen bonds : bond 0.04586 ( 238) hydrogen bonds : angle 3.84361 ( 714) *********************** 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 35 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.130 Fit side-chains REVERT: A 50 SER cc_start: 0.8010 (m) cc_final: 0.7662 (t) REVERT: B 50 SER cc_start: 0.7921 (m) cc_final: 0.7618 (t) REVERT: B 143 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (mt0) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.7526 time to fit residues: 26.3220 Evaluate side-chains 34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148669 restraints weight = 4172.527| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.16 r_work: 0.3578 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2307 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= 0.121 Angle : 0.466 4.118 5070 Z= 0.246 Chirality : 0.038 0.134 550 Planarity : 0.004 0.033 610 Dihedral : 4.170 15.122 560 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.54 % Allowed : 11.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.42), residues: 422 helix: 1.75 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.90 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 63 TYR 0.025 0.002 TYR A 86 PHE 0.010 0.001 PHE B 185 TRP 0.013 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3692) covalent geometry : angle 0.46615 ( 5070) hydrogen bonds : bond 0.03987 ( 238) hydrogen bonds : angle 3.75456 ( 714) *********************** 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 34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.133 Fit side-chains REVERT: A 50 SER cc_start: 0.7979 (m) cc_final: 0.7636 (t) REVERT: A 143 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: B 50 SER cc_start: 0.7884 (m) cc_final: 0.7588 (t) REVERT: B 143 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7925 (mt0) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.7067 time to fit residues: 24.0273 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN 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 39 optimal weight: 0.0370 chunk 29 optimal weight: 0.0370 chunk 26 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.163674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154036 restraints weight = 4101.782| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.12 r_work: 0.3653 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3692 Z= 0.094 Angle : 0.419 4.030 5070 Z= 0.226 Chirality : 0.036 0.129 550 Planarity : 0.004 0.035 610 Dihedral : 3.706 15.492 560 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.27 % Allowed : 12.63 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.42), residues: 422 helix: 2.01 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 1.12 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 171 TYR 0.011 0.001 TYR B 165 PHE 0.005 0.001 PHE B 185 TRP 0.019 0.001 TRP A 29 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3692) covalent geometry : angle 0.41937 ( 5070) hydrogen bonds : bond 0.03128 ( 238) hydrogen bonds : angle 3.57573 ( 714) *********************** 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 39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.128 Fit side-chains REVERT: A 50 SER cc_start: 0.7950 (m) cc_final: 0.7612 (t) REVERT: A 143 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: B 50 SER cc_start: 0.7853 (m) cc_final: 0.7559 (t) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.5745 time to fit residues: 23.1933 Evaluate side-chains 31 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.156723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147117 restraints weight = 4145.620| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.13 r_work: 0.3561 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2381 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= 0.143 Angle : 0.512 6.946 5070 Z= 0.264 Chirality : 0.039 0.135 550 Planarity : 0.004 0.033 610 Dihedral : 4.163 14.895 560 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 12.37 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.42), residues: 422 helix: 1.94 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.87 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.011 0.001 TYR A 165 PHE 0.015 0.001 PHE A 185 TRP 0.008 0.001 TRP A 29 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3692) covalent geometry : angle 0.51173 ( 5070) hydrogen bonds : bond 0.04231 ( 238) hydrogen bonds : angle 3.76285 ( 714) *********************** 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 34 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: A 50 SER cc_start: 0.7968 (m) cc_final: 0.7636 (t) REVERT: A 143 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: B 50 SER cc_start: 0.7871 (m) cc_final: 0.7575 (t) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.6387 time to fit residues: 22.4465 Evaluate side-chains 31 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.158551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148919 restraints weight = 4173.982| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.14 r_work: 0.3594 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2486 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 : 0.468 5.502 5070 Z= 0.245 Chirality : 0.038 0.130 550 Planarity : 0.004 0.033 610 Dihedral : 4.013 15.101 560 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.08 % Allowed : 12.90 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.42), residues: 422 helix: 1.98 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.90 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 17 TYR 0.024 0.002 TYR A 86 PHE 0.014 0.001 PHE B 185 TRP 0.013 0.001 TRP B 29 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3692) covalent geometry : angle 0.46824 ( 5070) hydrogen bonds : bond 0.03769 ( 238) hydrogen bonds : angle 3.70064 ( 714) ********************** 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 33 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.138 Fit side-chains REVERT: A 50 SER cc_start: 0.7975 (m) cc_final: 0.7639 (t) REVERT: A 143 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 50 SER cc_start: 0.7869 (m) cc_final: 0.7573 (t) outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.6234 time to fit residues: 21.3088 Evaluate side-chains 29 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149634 restraints weight = 4096.670| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.13 r_work: 0.3589 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2475 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= 0.111 Angle : 0.463 5.137 5070 Z= 0.244 Chirality : 0.038 0.130 550 Planarity : 0.004 0.032 610 Dihedral : 3.963 14.984 560 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.54 % Allowed : 12.90 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.42), residues: 422 helix: 2.03 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.88 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 17 TYR 0.011 0.001 TYR B 165 PHE 0.015 0.001 PHE B 185 TRP 0.013 0.001 TRP A 29 HIS 0.002 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3692) covalent geometry : angle 0.46333 ( 5070) hydrogen bonds : bond 0.03698 ( 238) hydrogen bonds : angle 3.68446 ( 714) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1373.05 seconds wall clock time: 23 minutes 57.11 seconds (1437.11 seconds total)