Starting phenix.real_space_refine on Thu Jul 18 21:28:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_2024/8k2w_36841.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_2024/8k2w_36841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_2024/8k2w_36841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_2024/8k2w_36841.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2w_36841/07_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 2.98, per 1000 atoms: 0.95 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 609.9 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: 0.35 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: 1.51 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: 93.70 - 101.78: 8 101.78 - 109.85: 387 109.85 - 117.93: 2044 117.93 - 126.00: 1875 126.00 - 134.07: 51 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 2.440 nonbonded pdb=" NH2 ARG R 216 " pdb=" OD2 ASP R 290 " model vdw 2.314 2.520 nonbonded pdb=" OG SER R 191 " pdb=" OD1 ASN R 206 " model vdw 2.347 2.440 nonbonded pdb=" O SER R 244 " pdb=" OG SER R 244 " model vdw 2.348 2.440 nonbonded pdb=" OG SER R 309 " pdb=" O3 FI6 R 404 " model vdw 2.393 2.440 ... (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 ========== 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: 0.910 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: 0.020 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.305 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: 0.7471 time to fit residues: 29.0835 Evaluate side-chains 30 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 GLN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1088 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= 0.214 Angle : 0.589 7.902 4365 Z= 0.284 Chirality : 0.039 0.127 503 Planarity : 0.004 0.033 522 Dihedral : 13.310 149.716 589 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.93 % Allowed : 11.25 % 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: 0.61 (0.45), residues: 378 helix: 1.43 (0.35), residues: 226 sheet: 0.76 (0.79), residues: 54 loop : -2.29 (0.57), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 106 HIS 0.003 0.001 HIS R 94 PHE 0.017 0.001 PHE R 207 TYR 0.012 0.001 TYR N 34 ARG 0.003 0.000 ARG R 259 *********************** 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 38 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.622 Fit side-chains REVERT: N 98 ASN cc_start: 0.7774 (t0) cc_final: 0.7101 (t0) REVERT: R 231 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7773 (mmt) REVERT: R 290 ASP cc_start: 0.5812 (m-30) cc_final: 0.5383 (m-30) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.7253 time to fit residues: 25.3626 Evaluate side-chains 35 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 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: 0.7739 moved from start: 0.1368 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= 0.193 Angle : 0.544 6.588 4365 Z= 0.267 Chirality : 0.038 0.128 503 Planarity : 0.003 0.031 522 Dihedral : 12.826 133.402 589 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.25 % Allowed : 13.83 % Favored : 83.92 % 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: 0.75 (0.45), residues: 378 helix: 1.51 (0.35), residues: 226 sheet: 0.66 (0.78), residues: 54 loop : -2.01 (0.59), 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 0.021 0.001 PHE R 207 TYR 0.010 0.001 TYR N 34 ARG 0.003 0.000 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 38 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.325 Fit side-chains REVERT: N 98 ASN cc_start: 0.7776 (t0) cc_final: 0.7126 (t0) REVERT: R 231 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7869 (mmt) REVERT: R 281 LEU cc_start: 0.8423 (mm) cc_final: 0.8196 (mt) REVERT: R 290 ASP cc_start: 0.5845 (m-30) cc_final: 0.5411 (m-30) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 0.6440 time to fit residues: 24.6630 Evaluate side-chains 33 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3212 Z= 0.161 Angle : 0.515 7.122 4365 Z= 0.253 Chirality : 0.037 0.124 503 Planarity : 0.003 0.030 522 Dihedral : 12.416 127.494 589 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 15.11 % Favored : 81.99 % 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: 0.96 (0.45), residues: 378 helix: 1.71 (0.35), residues: 226 sheet: 0.70 (0.77), residues: 54 loop : -2.02 (0.59), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 38 HIS 0.002 0.001 HIS R 94 PHE 0.018 0.001 PHE R 207 TYR 0.008 0.001 TYR N 34 ARG 0.002 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 fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.332 Fit side-chains REVERT: N 98 ASN cc_start: 0.7811 (t0) cc_final: 0.7279 (t0) REVERT: R 231 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7881 (mmt) REVERT: R 281 LEU cc_start: 0.8435 (mm) cc_final: 0.8210 (mt) REVERT: R 290 ASP cc_start: 0.5869 (m-30) cc_final: 0.5421 (m-30) outliers start: 9 outliers final: 2 residues processed: 36 average time/residue: 0.6835 time to fit residues: 26.1329 Evaluate side-chains 32 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.1679 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= 0.193 Angle : 0.546 7.362 4365 Z= 0.265 Chirality : 0.038 0.138 503 Planarity : 0.003 0.029 522 Dihedral : 12.180 124.004 589 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.25 % Allowed : 17.36 % 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: 0.77 (0.44), residues: 378 helix: 1.61 (0.35), residues: 228 sheet: 0.65 (0.77), residues: 54 loop : -2.35 (0.57), residues: 96 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 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 35 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.324 Fit side-chains REVERT: N 98 ASN cc_start: 0.7818 (t0) cc_final: 0.7099 (t0) REVERT: R 231 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7867 (mmt) REVERT: R 281 LEU cc_start: 0.8450 (mm) cc_final: 0.8229 (mt) REVERT: R 290 ASP cc_start: 0.5896 (m-30) cc_final: 0.5456 (m-30) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.6381 time to fit residues: 23.1360 Evaluate side-chains 33 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.1837 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= 0.217 Angle : 0.563 7.047 4365 Z= 0.276 Chirality : 0.039 0.138 503 Planarity : 0.004 0.028 522 Dihedral : 12.150 119.303 589 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.54 % Allowed : 16.40 % Favored : 80.06 % 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: 0.90 (0.45), residues: 378 helix: 1.67 (0.34), residues: 226 sheet: 0.76 (0.78), residues: 54 loop : -2.13 (0.59), residues: 98 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 0.002 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 38 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 0.323 Fit side-chains REVERT: N 98 ASN cc_start: 0.7832 (t0) cc_final: 0.7178 (t0) REVERT: R 231 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7885 (mmt) REVERT: R 281 LEU cc_start: 0.8423 (mm) cc_final: 0.8203 (mt) REVERT: R 290 ASP cc_start: 0.5953 (m-30) cc_final: 0.5541 (m-30) outliers start: 11 outliers final: 8 residues processed: 35 average time/residue: 0.5923 time to fit residues: 22.1288 Evaluate side-chains 36 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3212 Z= 0.253 Angle : 0.588 7.173 4365 Z= 0.287 Chirality : 0.040 0.138 503 Planarity : 0.004 0.028 522 Dihedral : 12.188 116.326 589 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.22 % Allowed : 17.36 % 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: 0.83 (0.44), residues: 378 helix: 1.63 (0.34), residues: 226 sheet: 0.75 (0.78), residues: 54 loop : -2.23 (0.58), 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 0.020 0.002 PHE R 207 TYR 0.011 0.002 TYR R 235 ARG 0.004 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 41 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.308 Fit side-chains REVERT: N 98 ASN cc_start: 0.7821 (t0) cc_final: 0.7104 (t0) REVERT: R 231 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7883 (mmt) REVERT: R 281 LEU cc_start: 0.8447 (mm) cc_final: 0.8216 (mt) REVERT: R 290 ASP cc_start: 0.5996 (m-30) cc_final: 0.5552 (m-30) REVERT: R 303 ARG cc_start: 0.6964 (mmt180) cc_final: 0.6605 (mmp-170) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.8702 time to fit residues: 34.5794 Evaluate side-chains 39 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3212 Z= 0.332 Angle : 0.654 7.747 4365 Z= 0.318 Chirality : 0.042 0.147 503 Planarity : 0.004 0.028 522 Dihedral : 12.390 113.772 589 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.54 % Allowed : 17.36 % Favored : 79.10 % 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: 0.39 (0.43), residues: 378 helix: 1.35 (0.34), residues: 229 sheet: 1.09 (0.87), residues: 45 loop : -2.71 (0.52), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.001 ARG R 259 *********************** 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 fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.409 Fit side-chains REVERT: N 98 ASN cc_start: 0.7807 (t0) cc_final: 0.7095 (t0) REVERT: R 231 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7905 (mmt) REVERT: R 281 LEU cc_start: 0.8459 (mm) cc_final: 0.8226 (mt) REVERT: R 290 ASP cc_start: 0.6048 (m-30) cc_final: 0.5632 (m-30) REVERT: R 303 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6664 (mmp-170) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 1.1093 time to fit residues: 43.8761 Evaluate side-chains 36 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER 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 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2136 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= 0.186 Angle : 0.552 7.387 4365 Z= 0.271 Chirality : 0.038 0.135 503 Planarity : 0.004 0.030 522 Dihedral : 11.940 103.001 589 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.89 % Allowed : 19.29 % Favored : 77.81 % 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: 0.88 (0.44), residues: 378 helix: 1.78 (0.34), residues: 226 sheet: 1.09 (0.84), residues: 45 loop : -2.39 (0.55), residues: 107 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 0.009 0.001 TYR N 34 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 36 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.336 Fit side-chains REVERT: N 98 ASN cc_start: 0.7817 (t0) cc_final: 0.7052 (t0) REVERT: R 231 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: R 281 LEU cc_start: 0.8428 (mm) cc_final: 0.8198 (mt) REVERT: R 290 ASP cc_start: 0.5988 (m-30) cc_final: 0.5577 (m-30) outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.7424 time to fit residues: 27.4296 Evaluate side-chains 31 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2205 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= 0.189 Angle : 0.575 7.380 4365 Z= 0.280 Chirality : 0.039 0.134 503 Planarity : 0.004 0.030 522 Dihedral : 11.530 93.234 589 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.25 % Allowed : 19.94 % Favored : 77.81 % 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: 0.93 (0.44), residues: 378 helix: 1.83 (0.34), residues: 226 sheet: 1.12 (0.85), residues: 45 loop : -2.40 (0.55), residues: 107 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 0.036 0.002 PHE R 189 TYR 0.009 0.001 TYR R 235 ARG 0.004 0.000 ARG R 212 ********************** 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 34 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.353 Fit side-chains REVERT: N 98 ASN cc_start: 0.7848 (t0) cc_final: 0.7261 (t0) REVERT: R 231 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7689 (mmm) REVERT: R 281 LEU cc_start: 0.8420 (mm) cc_final: 0.8190 (mt) REVERT: R 290 ASP cc_start: 0.6009 (m-30) cc_final: 0.5596 (m-30) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.7625 time to fit residues: 26.6324 Evaluate side-chains 32 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.181162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124865 restraints weight = 3051.106| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.07 r_work: 0.3276 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2238 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= 0.187 Angle : 0.565 7.688 4365 Z= 0.275 Chirality : 0.039 0.133 503 Planarity : 0.004 0.037 522 Dihedral : 11.194 83.670 589 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.57 % Allowed : 19.94 % Favored : 77.49 % 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: 1.01 (0.44), residues: 378 helix: 1.89 (0.34), residues: 227 sheet: 1.13 (0.84), residues: 45 loop : -2.39 (0.55), 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 0.028 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: 1300.90 seconds wall clock time: 23 minutes 39.43 seconds (1419.43 seconds total)