Starting phenix.real_space_refine on Wed Jan 15 10:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7y_44328/01_2025/9b7y_44328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7y_44328/01_2025/9b7y_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_44328/01_2025/9b7y_44328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7y_44328/01_2025/9b7y_44328.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7y_44328/01_2025/9b7y_44328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7y_44328/01_2025/9b7y_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-5571/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: 6.89, per 1000 atoms: 0.82 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: 2.41 Conformation dependent library (CDL) restraints added in 784.0 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: 3.47 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: 3.12 Time building geometry restraints manager: 2.73 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: 6.410 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- 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 : 0.773 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: 2.1427 time to fit residues: 91.7181 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 : 0.861 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089358 restraints weight = 11300.763| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.56 r_work: 0.3062 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.849 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7902 (ttm110) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 2.0285 time to fit residues: 95.6332 Evaluate side-chains 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.115384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085892 restraints weight = 11332.066| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.57 r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8749 Z= 0.279 Angle : 0.517 5.736 12371 Z= 0.296 Chirality : 0.034 0.122 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.362 175.644 2162 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.00 % Allowed : 14.38 % Favored : 84.62 % 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: 3.58 (0.31), residues: 758 helix: 2.92 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -0.02 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.015 0.002 TYR A 256 ARG 0.002 0.000 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 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (ttm170) REVERT: A 304 ARG cc_start: 0.8378 (ttt180) cc_final: 0.7995 (ttm110) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 2.0014 time to fit residues: 87.9256 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 : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG 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 36 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085326 restraints weight = 11316.653| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.56 r_work: 0.2991 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1168 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= 0.262 Angle : 0.516 6.591 12371 Z= 0.296 Chirality : 0.034 0.126 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.400 176.294 2162 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.34 % Allowed : 13.71 % 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: 3.55 (0.31), residues: 758 helix: 2.90 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.04 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.016 0.002 TYR A 256 ARG 0.003 0.000 ARG D 210 *********************** 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 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8636 (ttm170) REVERT: A 304 ARG cc_start: 0.8359 (ttt180) cc_final: 0.7983 (ttm110) REVERT: D 178 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7398 (mm-30) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 2.0765 time to fit residues: 91.3333 Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 A residue 294 ARG 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 29 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.115472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086051 restraints weight = 11250.673| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.56 r_work: 0.3004 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1170 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= 0.233 Angle : 0.501 6.764 12371 Z= 0.288 Chirality : 0.033 0.126 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.349 176.559 2162 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 13.88 % 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: 3.64 (0.31), residues: 758 helix: 3.00 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE D 32 TYR 0.014 0.002 TYR A 256 ARG 0.002 0.000 ARG A 128 *********************** 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 47 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8301 (ptm160) REVERT: A 294 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8608 (ttm170) REVERT: A 304 ARG cc_start: 0.8350 (ttt180) cc_final: 0.7979 (ttm110) REVERT: D 178 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7334 (mm-30) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 1.9518 time to fit residues: 90.0200 Evaluate side-chains 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG 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 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.114227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084730 restraints weight = 11241.097| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.56 r_work: 0.2979 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8749 Z= 0.283 Angle : 0.525 6.552 12371 Z= 0.300 Chirality : 0.034 0.122 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.354 176.825 2162 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.67 % Allowed : 14.05 % 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: 3.50 (0.31), residues: 758 helix: 2.87 (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 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE D 32 TYR 0.016 0.002 TYR A 256 ARG 0.003 0.000 ARG D 210 *********************** 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 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.830 Fit side-chains REVERT: A 89 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8249 (ptm160) REVERT: A 294 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8667 (ttm170) REVERT: D 178 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7394 (mm-30) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 2.1219 time to fit residues: 91.2039 Evaluate side-chains 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.114502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084988 restraints weight = 11276.008| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.56 r_work: 0.2984 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8749 Z= 0.251 Angle : 0.518 7.179 12371 Z= 0.296 Chirality : 0.034 0.123 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.351 176.866 2162 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.67 % Allowed : 14.05 % 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: 3.50 (0.31), residues: 758 helix: 2.88 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.04 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE D 32 TYR 0.016 0.002 TYR A 256 ARG 0.002 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 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.755 Fit side-chains REVERT: A 294 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8652 (ttm170) REVERT: D 178 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7450 (mm-30) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 1.9601 time to fit residues: 82.2524 Evaluate side-chains 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU 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 A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.115325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085795 restraints weight = 11420.471| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.58 r_work: 0.2997 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1281 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= 0.211 Angle : 0.500 7.263 12371 Z= 0.287 Chirality : 0.032 0.124 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.332 176.780 2162 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.67 % Allowed : 13.88 % 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: 3.64 (0.31), residues: 758 helix: 3.00 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.05 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.002 0.000 ARG A 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 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.728 Fit side-chains REVERT: A 89 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8295 (ptm160) REVERT: A 294 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (ttm170) REVERT: D 178 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7409 (mm-30) outliers start: 10 outliers final: 7 residues processed: 40 average time/residue: 2.1562 time to fit residues: 90.1876 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.115710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086265 restraints weight = 11366.132| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.57 r_work: 0.3001 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.004 0.037 8749 Z= 0.226 Angle : 0.496 7.208 12371 Z= 0.285 Chirality : 0.033 0.122 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.254 176.575 2162 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.51 % Allowed : 14.05 % 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: 3.68 (0.31), residues: 758 helix: 3.07 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE D 32 TYR 0.014 0.002 TYR A 256 ARG 0.002 0.000 ARG A 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 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.815 Fit side-chains REVERT: A 89 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8221 (ptm160) REVERT: A 294 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8581 (ttm170) REVERT: D 178 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7451 (mm-30) outliers start: 9 outliers final: 4 residues processed: 38 average time/residue: 2.1675 time to fit residues: 86.0340 Evaluate side-chains 37 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086321 restraints weight = 11375.663| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.57 r_work: 0.3002 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1302 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= 0.221 Angle : 0.495 7.587 12371 Z= 0.284 Chirality : 0.033 0.122 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.255 176.591 2162 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 3.69 (0.31), residues: 758 helix: 3.08 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.002 0.000 ARG D 114 ********************** 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 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.783 Fit side-chains REVERT: A 89 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8237 (ptm160) REVERT: A 294 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (ttm170) REVERT: D 178 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7472 (mm-30) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 2.3013 time to fit residues: 88.8570 Evaluate side-chains 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084716 restraints weight = 11386.937| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.57 r_work: 0.2977 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8749 Z= 0.285 Angle : 0.522 7.168 12371 Z= 0.299 Chirality : 0.034 0.120 1422 Planarity : 0.004 0.051 1180 Dihedral : 27.300 177.175 2162 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.34 % Allowed : 14.21 % 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: 3.51 (0.31), residues: 758 helix: 2.92 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.16 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE D 32 TYR 0.015 0.002 TYR A 256 ARG 0.002 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6666.36 seconds wall clock time: 118 minutes 24.60 seconds (7104.60 seconds total)