Starting phenix.real_space_refine on Sat Aug 3 00:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_43712.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_43712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_43712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_43712.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w0r_43712/08_2024/8w0r_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 Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 - 3.50 Amino acid : False - 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: 2.08 Conformation dependent library (CDL) restraints added in 805.8 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: 0.45 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: 1.09 Time building geometry restraints manager: 2.20 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: 100.83 - 107.52: 206 107.52 - 114.22: 2022 114.22 - 120.91: 1798 120.91 - 127.60: 954 127.60 - 134.29: 90 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: 0.00 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.940 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3692 Z= 0.294 Angle : 0.713 10.320 5070 Z= 0.349 Chirality : 0.109 1.692 550 Planarity : 0.006 0.055 610 Dihedral : 12.169 55.727 1314 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.43), residues: 422 helix: 0.44 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.61 (0.74), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 29 HIS 0.003 0.001 HIS A 76 PHE 0.009 0.001 PHE B 189 TYR 0.019 0.002 TYR B 86 ARG 0.007 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.7726 time to fit residues: 60.1154 Evaluate side-chains 31 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3692 Z= 0.162 Angle : 0.506 6.136 5070 Z= 0.268 Chirality : 0.040 0.143 550 Planarity : 0.005 0.039 610 Dihedral : 4.767 16.556 560 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.42), residues: 422 helix: 1.27 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 1.00 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.002 0.001 HIS A 30 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.002 TYR A 86 ARG 0.006 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.372 Fit side-chains REVERT: A 50 SER cc_start: 0.7753 (m) cc_final: 0.7274 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 1.7568 time to fit residues: 57.7890 Evaluate side-chains 29 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3692 Z= 0.271 Angle : 0.582 7.839 5070 Z= 0.297 Chirality : 0.042 0.150 550 Planarity : 0.005 0.038 610 Dihedral : 4.905 15.024 560 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.54 % Allowed : 8.06 % 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 (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: 1.94 (0.42), residues: 422 helix: 1.51 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.81 (0.68), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.004 0.001 HIS A 30 PHE 0.008 0.002 PHE B 117 TYR 0.021 0.002 TYR A 86 ARG 0.004 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.368 Fit side-chains REVERT: A 50 SER cc_start: 0.7887 (m) cc_final: 0.7535 (t) REVERT: B 50 SER cc_start: 0.7836 (m) cc_final: 0.7488 (t) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 1.4252 time to fit residues: 47.2584 Evaluate side-chains 33 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3692 Z= 0.148 Angle : 0.465 5.431 5070 Z= 0.242 Chirality : 0.038 0.146 550 Planarity : 0.004 0.035 610 Dihedral : 4.276 15.472 560 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.42), residues: 422 helix: 1.70 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.92 (0.69), 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 144 PHE 0.006 0.001 PHE A 189 TYR 0.021 0.002 TYR A 86 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.340 Fit side-chains REVERT: A 50 SER cc_start: 0.7793 (m) cc_final: 0.7431 (t) REVERT: B 50 SER cc_start: 0.7787 (m) cc_final: 0.7408 (t) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.4170 time to fit residues: 52.6220 Evaluate side-chains 33 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2192 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= 0.379 Angle : 0.643 7.277 5070 Z= 0.328 Chirality : 0.045 0.147 550 Planarity : 0.005 0.036 610 Dihedral : 4.970 15.294 560 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.61 % Allowed : 10.48 % 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: 1.80 (0.41), residues: 422 helix: 1.46 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.58 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 29 HIS 0.005 0.002 HIS A 76 PHE 0.012 0.002 PHE A 117 TYR 0.024 0.002 TYR B 86 ARG 0.004 0.001 ARG A 147 *********************** 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 42 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.397 Fit side-chains REVERT: A 50 SER cc_start: 0.7876 (m) cc_final: 0.7585 (t) REVERT: B 50 SER cc_start: 0.7839 (m) cc_final: 0.7566 (t) REVERT: B 143 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7550 (mt0) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 1.2645 time to fit residues: 52.3192 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 22 VAL 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 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2232 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= 0.166 Angle : 0.479 4.767 5070 Z= 0.251 Chirality : 0.038 0.136 550 Planarity : 0.004 0.034 610 Dihedral : 4.305 15.143 560 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.54 % Allowed : 11.29 % 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: 2.10 (0.41), residues: 422 helix: 1.68 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 0.62 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.002 0.001 HIS A 15 PHE 0.005 0.001 PHE A 191 TYR 0.022 0.002 TYR A 86 ARG 0.001 0.000 ARG B 26 *********************** 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 38 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.387 Fit side-chains REVERT: A 50 SER cc_start: 0.7823 (m) cc_final: 0.7519 (t) REVERT: B 50 SER cc_start: 0.7780 (m) cc_final: 0.7495 (t) REVERT: B 143 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7482 (mt0) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 1.2011 time to fit residues: 44.9132 Evaluate side-chains 36 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2263 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= 0.190 Angle : 0.491 4.430 5070 Z= 0.259 Chirality : 0.039 0.135 550 Planarity : 0.004 0.034 610 Dihedral : 4.267 14.948 560 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.81 % Allowed : 11.29 % 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: 1.74 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 0.61 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.010 0.001 PHE B 185 TYR 0.013 0.001 TYR B 165 ARG 0.002 0.000 ARG B 147 *********************** 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 39 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.378 Fit side-chains REVERT: A 50 SER cc_start: 0.7813 (m) cc_final: 0.7525 (t) REVERT: B 50 SER cc_start: 0.7714 (m) cc_final: 0.7438 (t) REVERT: B 143 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7559 (mt0) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 1.2314 time to fit residues: 45.9262 Evaluate side-chains 36 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ARG 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 3 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3692 Z= 0.183 Angle : 0.482 4.360 5070 Z= 0.254 Chirality : 0.039 0.132 550 Planarity : 0.004 0.034 610 Dihedral : 4.197 14.983 560 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 2.24 (0.41), residues: 422 helix: 1.73 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.82 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.002 0.001 HIS A 15 PHE 0.011 0.001 PHE B 185 TYR 0.026 0.002 TYR A 86 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.379 Fit side-chains REVERT: A 50 SER cc_start: 0.7825 (m) cc_final: 0.7543 (t) REVERT: B 50 SER cc_start: 0.7753 (m) cc_final: 0.7486 (t) REVERT: B 143 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7533 (mt0) outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 1.1312 time to fit residues: 42.3711 Evaluate side-chains 33 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ARG 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 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 18 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2442 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= 0.137 Angle : 0.443 3.978 5070 Z= 0.237 Chirality : 0.037 0.127 550 Planarity : 0.004 0.034 610 Dihedral : 3.867 15.117 560 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.54 % Allowed : 12.10 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.41), residues: 422 helix: 1.91 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.93 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 29 HIS 0.001 0.001 HIS B 30 PHE 0.009 0.001 PHE B 185 TYR 0.012 0.001 TYR B 165 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.355 Fit side-chains REVERT: A 50 SER cc_start: 0.7801 (m) cc_final: 0.7521 (t) REVERT: B 50 SER cc_start: 0.7689 (m) cc_final: 0.7417 (t) REVERT: B 143 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7506 (mt0) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 1.0161 time to fit residues: 41.3147 Evaluate side-chains 32 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ARG 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 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2440 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= 0.190 Angle : 0.501 6.928 5070 Z= 0.259 Chirality : 0.039 0.130 550 Planarity : 0.004 0.034 610 Dihedral : 4.104 14.901 560 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 (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: 2.44 (0.41), residues: 422 helix: 1.90 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.81 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.001 PHE B 185 TYR 0.012 0.001 TYR A 165 ARG 0.003 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.338 Fit side-chains REVERT: A 50 SER cc_start: 0.7825 (m) cc_final: 0.7544 (t) REVERT: B 50 SER cc_start: 0.7699 (m) cc_final: 0.7428 (t) REVERT: B 143 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7461 (mt0) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 1.2108 time to fit residues: 38.9974 Evaluate side-chains 32 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ARG 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 29 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 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 = 0.3750 r_free = 0.3750 target = 0.157104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147543 restraints weight = 4115.558| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.13 r_work: 0.3572 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2446 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= 0.172 Angle : 0.488 5.923 5070 Z= 0.254 Chirality : 0.038 0.129 550 Planarity : 0.004 0.033 610 Dihedral : 4.067 14.884 560 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.54 % Allowed : 13.17 % Favored : 86.29 % 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: 2.46 (0.41), residues: 422 helix: 1.92 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.78 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.002 0.001 HIS B 15 PHE 0.014 0.001 PHE B 185 TYR 0.012 0.001 TYR B 165 ARG 0.003 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1484.52 seconds wall clock time: 26 minutes 46.33 seconds (1606.33 seconds total)