Starting phenix.real_space_refine on Fri Dec 27 09:05:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.map" model { file = "/net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k2w_36841/12_2024/8k2w_36841.cif" } resolution = 3.0 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= -0.002 sd= 0.152 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2063 2.51 5 N 525 2.21 5 O 532 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2223 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "R" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'CLR': 1, 'FI6': 1, 'LPC': 1, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.04, per 1000 atoms: 0.97 Number of scatterers: 3143 At special positions: 0 Unit cell: (68.85, 53.55, 118.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 2 15.00 F 3 9.00 O 532 8.00 N 525 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 302.3 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 3 sheets defined 63.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 55 through 81 removed outlier: 4.001A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 104 Processing helix chain 'R' and resid 105 through 115 removed outlier: 3.600A pdb=" N TRP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 155 removed outlier: 3.892A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 189 removed outlier: 3.526A pdb=" N THR R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 182 " --> pdb=" O LEU R 178 " (cutoff:3.500A) Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 208 through 244 removed outlier: 3.738A pdb=" N ALA R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Proline residue: R 227 - end of helix removed outlier: 4.063A pdb=" N SER R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 292 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 330 removed outlier: 4.259A pdb=" N ARG R 303 " --> pdb=" O GLY R 299 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 304 " --> pdb=" O ARG R 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 removed outlier: 3.790A pdb=" N ARG R 334 " --> pdb=" O GLY R 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER N 27 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 22 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61 removed outlier: 3.788A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG N 32 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU N 100 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET N 36 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN N 98 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP N 38 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR N 96 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61 removed outlier: 3.788A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG N 32 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU N 100 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET N 36 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN N 98 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP N 38 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR N 96 " --> pdb=" O TRP N 38 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 458 1.31 - 1.43: 907 1.43 - 1.56: 1818 1.56 - 1.68: 5 1.68 - 1.81: 24 Bond restraints: 3212 Sorted by residual: bond pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.70e+01 bond pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C11 PCW R 402 " pdb=" O3 PCW R 402 " ideal model delta sigma weight residual 1.326 1.414 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 PCW R 402 " pdb=" O2 PCW R 402 " ideal model delta sigma weight residual 1.333 1.403 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N PCW R 402 " pdb=" C6 PCW R 402 " ideal model delta sigma weight residual 1.489 1.439 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 4299 3.00 - 6.00: 54 6.00 - 9.00: 5 9.00 - 12.00: 2 12.00 - 15.00: 5 Bond angle restraints: 4365 Sorted by residual: angle pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " pdb=" C21 PCW R 402 " ideal model delta sigma weight residual 127.82 112.82 15.00 3.00e+00 1.11e-01 2.50e+01 angle pdb=" C18 PCW R 402 " pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " ideal model delta sigma weight residual 127.82 112.95 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C38 PCW R 402 " pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " ideal model delta sigma weight residual 127.57 112.87 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " pdb=" C41 PCW R 402 " ideal model delta sigma weight residual 127.60 113.22 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O3P PCW R 402 " pdb=" P PCW R 402 " pdb=" O4P PCW R 402 " ideal model delta sigma weight residual 96.85 110.25 -13.40 3.00e+00 1.11e-01 1.99e+01 ... (remaining 4360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 1893 34.51 - 69.03: 43 69.03 - 103.54: 4 103.54 - 138.05: 0 138.05 - 172.57: 1 Dihedral angle restraints: 1941 sinusoidal: 826 harmonic: 1115 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" C2 PCW R 402 " pdb=" C31 PCW R 402 " pdb=" O2 PCW R 402 " pdb=" C32 PCW R 402 " ideal model delta sinusoidal sigma weight residual 175.43 -12.00 -172.57 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA LEU R 294 " pdb=" C LEU R 294 " pdb=" N ALA R 295 " pdb=" CA ALA R 295 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 1938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 360 0.039 - 0.079: 109 0.079 - 0.118: 30 0.118 - 0.157: 3 0.157 - 0.196: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" C2 PCW R 402 " pdb=" C1 PCW R 402 " pdb=" C3 PCW R 402 " pdb=" O2 PCW R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA VAL R 245 " pdb=" N VAL R 245 " pdb=" C VAL R 245 " pdb=" CB VAL R 245 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 500 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW R 402 " -0.318 2.00e-02 2.50e+03 3.16e-01 1.00e+03 pdb=" C19 PCW R 402 " 0.321 2.00e-02 2.50e+03 pdb=" C20 PCW R 402 " 0.311 2.00e-02 2.50e+03 pdb=" C21 PCW R 402 " -0.315 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW R 402 " 0.198 2.00e-02 2.50e+03 1.98e-01 3.91e+02 pdb=" C39 PCW R 402 " -0.197 2.00e-02 2.50e+03 pdb=" C40 PCW R 402 " -0.198 2.00e-02 2.50e+03 pdb=" C41 PCW R 402 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 FI6 R 404 " -0.075 2.00e-02 2.50e+03 7.99e-02 9.58e+01 pdb=" C18 FI6 R 404 " 0.109 2.00e-02 2.50e+03 pdb=" C24 FI6 R 404 " -0.031 2.00e-02 2.50e+03 pdb=" C25 FI6 R 404 " 0.110 2.00e-02 2.50e+03 pdb=" N4 FI6 R 404 " -0.031 2.00e-02 2.50e+03 pdb=" O3 FI6 R 404 " -0.082 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 834 2.82 - 3.34: 2889 3.34 - 3.86: 4933 3.86 - 4.38: 5486 4.38 - 4.90: 9812 Nonbonded interactions: 23954 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG R 216 " pdb=" OD2 ASP R 290 " model vdw 2.314 3.120 nonbonded pdb=" OG SER R 191 " pdb=" OD1 ASN R 206 " model vdw 2.347 3.040 nonbonded pdb=" O SER R 244 " pdb=" OG SER R 244 " model vdw 2.348 3.040 nonbonded pdb=" OG SER R 309 " pdb=" O3 FI6 R 404 " model vdw 2.393 3.040 ... (remaining 23949 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.270 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.007 0.197 3212 Z= 0.399 Angle : 0.896 15.004 4365 Z= 0.367 Chirality : 0.040 0.196 503 Planarity : 0.017 0.316 522 Dihedral : 15.069 172.568 1219 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.73 (0.45), residues: 378 helix: 1.50 (0.36), residues: 222 sheet: 0.17 (0.77), residues: 53 loop : -1.58 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 106 HIS 0.003 0.001 HIS R 193 PHE 0.016 0.001 PHE R 207 TYR 0.010 0.001 TYR R 235 ARG 0.002 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.335 Fit side-chains REVERT: N 98 ASN cc_start: 0.7673 (t0) cc_final: 0.7254 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.7714 time to fit residues: 30.0075 Evaluate side-chains 30 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3212 Z= 0.198 Angle : 0.586 7.962 4365 Z= 0.284 Chirality : 0.039 0.137 503 Planarity : 0.004 0.027 522 Dihedral : 13.344 147.027 589 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.61 % Allowed : 11.58 % Favored : 86.82 % 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: 0.58 (0.45), residues: 378 helix: 1.44 (0.35), residues: 226 sheet: 0.68 (0.78), residues: 54 loop : -2.34 (0.56), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 38 HIS 0.003 0.001 HIS R 94 PHE 0.019 0.001 PHE R 207 TYR 0.013 0.001 TYR N 34 ARG 0.003 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.389 Fit side-chains REVERT: N 98 ASN cc_start: 0.7720 (t0) cc_final: 0.7157 (t0) REVERT: R 231 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7772 (mmt) REVERT: R 290 ASP cc_start: 0.5884 (m-30) cc_final: 0.5410 (m-30) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.7236 time to fit residues: 26.9441 Evaluate side-chains 32 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3212 Z= 0.348 Angle : 0.681 7.965 4365 Z= 0.333 Chirality : 0.043 0.149 503 Planarity : 0.004 0.029 522 Dihedral : 13.378 140.806 589 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.89 % Allowed : 13.83 % Favored : 83.28 % 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: 0.11 (0.43), residues: 378 helix: 0.98 (0.34), residues: 230 sheet: 0.53 (0.78), residues: 54 loop : -2.45 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 38 HIS 0.005 0.001 HIS R 94 PHE 0.025 0.002 PHE R 207 TYR 0.015 0.002 TYR R 235 ARG 0.005 0.001 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.249 Fit side-chains REVERT: N 98 ASN cc_start: 0.7807 (t0) cc_final: 0.7173 (t0) REVERT: R 95 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8489 (mt) REVERT: R 231 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7869 (mmt) REVERT: R 260 ARG cc_start: 0.7271 (mtm-85) cc_final: 0.7052 (mtp180) REVERT: R 303 ARG cc_start: 0.6926 (mmt180) cc_final: 0.6661 (mmp-170) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.1176 time to fit residues: 45.0584 Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3212 Z= 0.208 Angle : 0.562 6.573 4365 Z= 0.280 Chirality : 0.039 0.136 503 Planarity : 0.004 0.032 522 Dihedral : 13.052 134.859 589 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.89 % Allowed : 16.40 % Favored : 80.71 % 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: 0.54 (0.44), residues: 378 helix: 1.39 (0.35), residues: 227 sheet: 0.54 (0.76), residues: 54 loop : -2.27 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 38 HIS 0.002 0.001 HIS R 94 PHE 0.019 0.002 PHE R 207 TYR 0.010 0.001 TYR N 34 ARG 0.003 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.317 Fit side-chains REVERT: N 98 ASN cc_start: 0.7830 (t0) cc_final: 0.7193 (t0) REVERT: R 231 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7883 (mmt) REVERT: R 290 ASP cc_start: 0.5802 (m-30) cc_final: 0.5311 (m-30) REVERT: R 303 ARG cc_start: 0.6963 (mmt180) cc_final: 0.6587 (mmp-170) outliers start: 9 outliers final: 3 residues processed: 36 average time/residue: 0.8222 time to fit residues: 31.0157 Evaluate side-chains 33 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3212 Z= 0.228 Angle : 0.580 7.000 4365 Z= 0.285 Chirality : 0.040 0.145 503 Planarity : 0.004 0.032 522 Dihedral : 12.878 133.081 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.50 % Allowed : 16.08 % Favored : 79.42 % 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: 0.44 (0.44), residues: 378 helix: 1.35 (0.34), residues: 229 sheet: 0.62 (0.76), residues: 54 loop : -2.57 (0.55), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 38 HIS 0.003 0.001 HIS R 94 PHE 0.020 0.002 PHE R 207 TYR 0.011 0.001 TYR R 235 ARG 0.004 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.358 Fit side-chains REVERT: N 98 ASN cc_start: 0.7838 (t0) cc_final: 0.7155 (t0) REVERT: R 231 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7884 (mmt) REVERT: R 252 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6417 (mtp180) REVERT: R 290 ASP cc_start: 0.5828 (m-30) cc_final: 0.5362 (m-30) REVERT: R 303 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6629 (mmp-170) outliers start: 14 outliers final: 7 residues processed: 39 average time/residue: 0.8325 time to fit residues: 34.0588 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3212 Z= 0.213 Angle : 0.564 6.799 4365 Z= 0.278 Chirality : 0.039 0.140 503 Planarity : 0.004 0.033 522 Dihedral : 12.675 131.200 589 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.54 % Allowed : 16.08 % Favored : 80.39 % 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: 0.70 (0.44), residues: 378 helix: 1.54 (0.34), residues: 227 sheet: 0.66 (0.76), residues: 54 loop : -2.31 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 38 HIS 0.003 0.001 HIS R 94 PHE 0.019 0.001 PHE R 207 TYR 0.010 0.001 TYR R 235 ARG 0.003 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.330 Fit side-chains REVERT: N 98 ASN cc_start: 0.7850 (t0) cc_final: 0.7143 (t0) REVERT: R 231 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7929 (mmt) REVERT: R 252 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6430 (mtp180) REVERT: R 290 ASP cc_start: 0.5853 (m-30) cc_final: 0.5395 (m-30) outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 0.7789 time to fit residues: 27.9283 Evaluate side-chains 35 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3212 Z= 0.305 Angle : 0.636 7.779 4365 Z= 0.310 Chirality : 0.041 0.144 503 Planarity : 0.004 0.033 522 Dihedral : 12.799 133.852 589 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.50 % Allowed : 16.08 % Favored : 79.42 % 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: 0.28 (0.43), residues: 378 helix: 1.26 (0.34), residues: 230 sheet: 1.08 (0.84), residues: 45 loop : -2.78 (0.51), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 38 HIS 0.004 0.001 HIS R 94 PHE 0.021 0.002 PHE R 207 TYR 0.013 0.002 TYR R 235 ARG 0.006 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.329 Fit side-chains REVERT: N 98 ASN cc_start: 0.7831 (t0) cc_final: 0.7056 (t0) REVERT: R 231 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: R 252 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6494 (mtp180) REVERT: R 290 ASP cc_start: 0.5950 (m-30) cc_final: 0.5464 (m-30) REVERT: R 303 ARG cc_start: 0.7027 (mmt180) cc_final: 0.6646 (mmp-170) outliers start: 14 outliers final: 8 residues processed: 39 average time/residue: 0.9021 time to fit residues: 36.8349 Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3212 Z= 0.185 Angle : 0.572 6.811 4365 Z= 0.282 Chirality : 0.039 0.136 503 Planarity : 0.004 0.032 522 Dihedral : 12.464 129.339 589 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.54 % Allowed : 18.01 % Favored : 78.46 % 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: 0.74 (0.44), residues: 378 helix: 1.62 (0.34), residues: 227 sheet: 1.15 (0.84), residues: 45 loop : -2.41 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 PHE 0.034 0.002 PHE R 189 TYR 0.009 0.001 TYR N 34 ARG 0.003 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: N 98 ASN cc_start: 0.7862 (t0) cc_final: 0.7276 (t0) REVERT: R 231 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7668 (mmm) REVERT: R 290 ASP cc_start: 0.5871 (m-30) cc_final: 0.5419 (m-30) outliers start: 11 outliers final: 7 residues processed: 39 average time/residue: 0.8439 time to fit residues: 34.3947 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3212 Z= 0.220 Angle : 0.595 7.760 4365 Z= 0.290 Chirality : 0.039 0.134 503 Planarity : 0.004 0.032 522 Dihedral : 12.401 128.548 589 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.78 % 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: 0.77 (0.44), residues: 378 helix: 1.65 (0.34), residues: 227 sheet: 1.17 (0.84), residues: 45 loop : -2.44 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 338 HIS 0.003 0.001 HIS R 94 PHE 0.028 0.002 PHE R 189 TYR 0.010 0.001 TYR R 235 ARG 0.003 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.354 Fit side-chains REVERT: N 98 ASN cc_start: 0.7856 (t0) cc_final: 0.7115 (t0) REVERT: R 231 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7713 (mmm) REVERT: R 290 ASP cc_start: 0.5889 (m-30) cc_final: 0.5433 (m-30) outliers start: 11 outliers final: 8 residues processed: 36 average time/residue: 0.7074 time to fit residues: 26.9490 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0010 chunk 5 optimal weight: 6.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3212 Z= 0.148 Angle : 0.537 7.657 4365 Z= 0.264 Chirality : 0.038 0.131 503 Planarity : 0.004 0.036 522 Dihedral : 12.006 122.514 589 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 18.33 % Favored : 78.46 % 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: 1.05 (0.45), residues: 378 helix: 1.92 (0.35), residues: 225 sheet: 0.75 (0.74), residues: 54 loop : -2.35 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 338 HIS 0.002 0.001 HIS R 202 PHE 0.020 0.001 PHE R 189 TYR 0.009 0.001 TYR N 34 ARG 0.001 0.000 ARG R 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.320 Fit side-chains REVERT: N 98 ASN cc_start: 0.7890 (t0) cc_final: 0.7287 (t0) REVERT: R 231 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: R 290 ASP cc_start: 0.5799 (m-30) cc_final: 0.5335 (m-30) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.6730 time to fit residues: 29.2065 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 0 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.182247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125316 restraints weight = 3046.963| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.11 r_work: 0.3284 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3212 Z= 0.168 Angle : 0.562 7.966 4365 Z= 0.270 Chirality : 0.038 0.129 503 Planarity : 0.004 0.036 522 Dihedral : 11.856 120.557 589 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.93 % Allowed : 21.54 % Favored : 76.53 % 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: 0.98 (0.44), residues: 378 helix: 1.84 (0.34), residues: 227 sheet: 1.20 (0.82), residues: 45 loop : -2.38 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 338 HIS 0.002 0.001 HIS R 202 PHE 0.020 0.002 PHE R 189 TYR 0.009 0.001 TYR R 235 ARG 0.003 0.000 ARG R 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1282.41 seconds wall clock time: 23 minutes 50.75 seconds (1430.75 seconds total)