Starting phenix.real_space_refine on Sat Dec 28 10:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7y_44328/12_2024/9b7y_44328.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 120 5.49 5 S 12 5.16 5 C 4863 2.51 5 N 1562 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2954 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2947 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 640 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 599 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Time building chain proxies: 7.23, per 1000 atoms: 0.86 Number of scatterers: 8361 At special positions: 0 Unit cell: (155.8, 99.75, 92.15, 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 P 120 15.00 O 1804 8.00 N 1562 7.00 C 4863 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: 2.36 Conformation dependent library (CDL) restraints added in 751.0 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.3% alpha, 0.0% beta 46 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 Processing helix chain 'A' and resid 36 through 44 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.575A pdb=" N LEU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 Processing helix chain 'A' and resid 90 through 105 removed outlier: 4.836A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.060A pdb=" N TRP A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 120 through 146 Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.683A pdb=" N HIS A 171 " --> pdb=" O LEU A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 234 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 288 removed outlier: 3.511A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 324 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.795A pdb=" N ARG A 380 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.741A pdb=" N GLU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'D' and resid 14 through 30 Processing helix chain 'D' and resid 36 through 44 Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.815A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 78 Processing helix chain 'D' and resid 90 through 105 removed outlier: 5.172A pdb=" N GLU D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.694A pdb=" N THR D 109 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 120 through 146 Processing helix chain 'D' and resid 150 through 169 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.875A pdb=" N VAL D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.625A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 261 through 288 removed outlier: 4.013A pdb=" N ILE D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 320 through 323 Processing helix chain 'D' and resid 324 through 350 Processing helix chain 'D' and resid 354 through 375 Processing helix chain 'D' and resid 376 through 380 removed outlier: 3.786A pdb=" N ARG D 380 " --> pdb=" O HIS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 398 removed outlier: 3.747A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1166 1.32 - 1.44: 2839 1.44 - 1.56: 4492 1.56 - 1.69: 236 1.69 - 1.81: 16 Bond restraints: 8749 Sorted by residual: bond pdb=" C LEU A 95 " pdb=" O LEU A 95 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C ALA A 102 " pdb=" O ALA A 102 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N ARG A 89 " pdb=" CA ARG A 89 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.23e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.46e-02 4.69e+03 5.67e+00 bond pdb=" N ASP A 211 " pdb=" CA ASP A 211 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.63e+00 ... (remaining 8744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 12061 1.78 - 3.56: 287 3.56 - 5.34: 17 5.34 - 7.12: 4 7.12 - 8.89: 2 Bond angle restraints: 12371 Sorted by residual: angle pdb=" N GLN A 113 " pdb=" CA GLN A 113 " pdb=" C GLN A 113 " ideal model delta sigma weight residual 111.36 118.55 -7.19 1.09e+00 8.42e-01 4.35e+01 angle pdb=" N ALA D 48 " pdb=" CA ALA D 48 " pdb=" C ALA D 48 " ideal model delta sigma weight residual 111.33 118.33 -7.00 1.21e+00 6.83e-01 3.35e+01 angle pdb=" N ARG D 106 " pdb=" CA ARG D 106 " pdb=" C ARG D 106 " ideal model delta sigma weight residual 111.28 116.98 -5.70 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N LEU A 108 " pdb=" CA LEU A 108 " pdb=" C LEU A 108 " ideal model delta sigma weight residual 113.19 118.60 -5.41 1.19e+00 7.06e-01 2.07e+01 angle pdb=" N ARG A 106 " pdb=" CA ARG A 106 " pdb=" C ARG A 106 " ideal model delta sigma weight residual 111.28 116.05 -4.77 1.09e+00 8.42e-01 1.91e+01 ... (remaining 12366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 4343 34.84 - 69.67: 611 69.67 - 104.51: 10 104.51 - 139.34: 2 139.34 - 174.18: 3 Dihedral angle restraints: 4969 sinusoidal: 2741 harmonic: 2228 Sorted by residual: dihedral pdb=" C4' DG F 33 " pdb=" C3' DG F 33 " pdb=" O3' DG F 33 " pdb=" P DC F 34 " ideal model delta sinusoidal sigma weight residual 220.00 45.82 174.18 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC C 10 " pdb=" C3' DC C 10 " pdb=" O3' DC C 10 " pdb=" P DC C 11 " ideal model delta sinusoidal sigma weight residual 220.00 49.27 170.73 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG F 35 " pdb=" C3' DG F 35 " pdb=" O3' DG F 35 " pdb=" P DA F 36 " ideal model delta sinusoidal sigma weight residual 220.00 73.23 146.77 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1302 0.066 - 0.132: 105 0.132 - 0.198: 7 0.198 - 0.264: 5 0.264 - 0.330: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA TRP A 112 " pdb=" N TRP A 112 " pdb=" C TRP A 112 " pdb=" CB TRP A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C3' DC C 10 " pdb=" C4' DC C 10 " pdb=" O3' DC C 10 " pdb=" C2' DC C 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DG F 33 " pdb=" C4' DG F 33 " pdb=" O3' DG F 33 " pdb=" C2' DG F 33 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1419 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 252 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 253 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 89 " -0.196 9.50e-02 1.11e+02 8.78e-02 4.73e+00 pdb=" NE ARG A 89 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 89 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 89 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 89 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 107 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C ALA A 107 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 107 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 108 " -0.010 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2558 2.85 - 3.36: 7612 3.36 - 3.87: 15605 3.87 - 4.39: 17403 4.39 - 4.90: 26826 Nonbonded interactions: 70004 Sorted by model distance: nonbonded pdb=" N4 DC B 106 " pdb=" O6 DG C 18 " model vdw 2.333 3.120 nonbonded pdb=" N6 DA B 110 " pdb=" O4 DT C 14 " model vdw 2.337 3.120 nonbonded pdb=" OE1 GLN A 335 " pdb=" NH2 ARG A 338 " model vdw 2.348 3.120 nonbonded pdb=" N GLU D 178 " pdb=" OE1 GLU D 178 " model vdw 2.351 3.120 nonbonded pdb=" O4 DT B 96 " pdb=" N6 DA C 28 " model vdw 2.377 3.120 ... (remaining 69999 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' and (resid 8 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 211 or (resid 212 throu \ gh 213 and (name N or name CA or name C or name O or name CB )) or resid 214 thr \ ough 401)) selection = (chain 'D' and (resid 8 through 209 or (resid 210 and (name N or name CA or name \ C or name O or name CB )) or resid 211 through 401)) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 86 through 114) } ncs_group { reference = chain 'C' selection = (chain 'F' and resid 10 through 38) } 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: 8.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.700 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.004 0.041 8749 Z= 0.239 Angle : 0.580 8.895 12371 Z= 0.378 Chirality : 0.041 0.330 1422 Planarity : 0.005 0.088 1180 Dihedral : 24.660 174.178 3525 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.31), residues: 758 helix: 2.87 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.16 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 112 HIS 0.001 0.000 HIS D 54 PHE 0.009 0.001 PHE D 32 TYR 0.008 0.001 TYR A 256 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7764 (ttm110) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 2.2602 time to fit residues: 96.7562 Evaluate side-chains 35 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8749 Z= 0.182 Angle : 0.490 5.999 12371 Z= 0.280 Chirality : 0.032 0.125 1422 Planarity : 0.004 0.054 1180 Dihedral : 27.300 176.880 2162 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 14.05 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.31), residues: 758 helix: 3.08 (0.21), residues: 596 sheet: None (None), residues: 0 loop : 0.14 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.002 0.001 HIS D 54 PHE 0.009 0.001 PHE D 32 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 2.0056 time to fit residues: 94.6528 Evaluate side-chains 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8749 Z= 0.346 Angle : 0.561 5.882 12371 Z= 0.319 Chirality : 0.037 0.125 1422 Planarity : 0.005 0.052 1180 Dihedral : 27.455 176.393 2162 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.17 % Allowed : 14.38 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.31), residues: 758 helix: 2.86 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.07 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.012 0.002 PHE D 32 TYR 0.016 0.002 TYR A 256 ARG 0.003 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 2.1039 time to fit residues: 83.9239 Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.222 Angle : 0.500 5.351 12371 Z= 0.288 Chirality : 0.033 0.126 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.398 176.094 2162 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.00 % Allowed : 14.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.31), residues: 758 helix: 2.99 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.13 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.017 0.002 TYR A 256 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.815 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 1.9657 time to fit residues: 84.5619 Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8749 Z= 0.212 Angle : 0.495 7.083 12371 Z= 0.284 Chirality : 0.032 0.126 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.332 176.131 2162 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.34 % Allowed : 14.38 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.31), residues: 758 helix: 3.05 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.09 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.015 0.002 TYR A 256 ARG 0.003 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.825 Fit side-chains REVERT: A 214 ASP cc_start: 0.8305 (m-30) cc_final: 0.7854 (p0) REVERT: D 181 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7964 (tttm) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 1.9182 time to fit residues: 82.6408 Evaluate side-chains 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8749 Z= 0.163 Angle : 0.472 7.216 12371 Z= 0.271 Chirality : 0.031 0.129 1422 Planarity : 0.004 0.054 1180 Dihedral : 27.219 175.230 2162 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.34 % Allowed : 14.38 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 758 helix: 3.15 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.17 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.002 0.000 HIS D 377 PHE 0.008 0.001 PHE D 32 TYR 0.015 0.001 TYR A 256 ARG 0.001 0.000 ARG D 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.842 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 1.8223 time to fit residues: 80.7981 Evaluate side-chains 37 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 70 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.2928 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8749 Z= 0.161 Angle : 0.468 6.926 12371 Z= 0.269 Chirality : 0.031 0.127 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.142 174.841 2162 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.84 % Allowed : 15.38 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.31), residues: 758 helix: 3.24 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.17 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.002 0.000 HIS A 54 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR D 256 ARG 0.003 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.820 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 1.9996 time to fit residues: 81.9860 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8749 Z= 0.235 Angle : 0.494 6.699 12371 Z= 0.283 Chirality : 0.033 0.122 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.171 175.317 2162 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.50 % Allowed : 16.05 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.31), residues: 758 helix: 3.15 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.11 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.012 0.002 TYR D 256 ARG 0.004 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.726 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 2.0736 time to fit residues: 80.5120 Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8749 Z= 0.208 Angle : 0.490 7.338 12371 Z= 0.281 Chirality : 0.032 0.123 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.173 175.395 2162 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 15.72 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.31), residues: 758 helix: 3.16 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.11 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.012 0.002 TYR D 256 ARG 0.004 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.738 Fit side-chains outliers start: 4 outliers final: 5 residues processed: 37 average time/residue: 2.0822 time to fit residues: 80.6658 Evaluate side-chains 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8749 Z= 0.179 Angle : 0.479 7.527 12371 Z= 0.276 Chirality : 0.031 0.125 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.159 175.368 2162 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.67 % Allowed : 15.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.31), residues: 758 helix: 3.17 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.11 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.002 0.000 HIS A 54 PHE 0.009 0.001 PHE D 32 TYR 0.011 0.001 TYR D 256 ARG 0.004 0.000 ARG D 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.769 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 2.1315 time to fit residues: 80.6131 Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.115985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086465 restraints weight = 11200.131| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.55 r_work: 0.3012 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8749 Z= 0.220 Angle : 0.495 7.290 12371 Z= 0.284 Chirality : 0.032 0.122 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.177 175.925 2162 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 15.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.31), residues: 758 helix: 3.04 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.03 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.012 0.002 TYR D 256 ARG 0.004 0.000 ARG D 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.92 seconds wall clock time: 48 minutes 34.12 seconds (2914.12 seconds total)