Starting phenix.real_space_refine on Fri May 9 20:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k2w_36841/05_2025/8k2w_36841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k2w_36841/05_2025/8k2w_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_36841/05_2025/8k2w_36841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k2w_36841/05_2025/8k2w_36841.map" model { file = "/net/cci-nas-00/data/ceres_data/8k2w_36841/05_2025/8k2w_36841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k2w_36841/05_2025/8k2w_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-5687/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: 3.05, 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: 1.04 Conformation dependent library (CDL) restraints added in 392.8 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: 0.28 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: 0.79 Time building geometry restraints manager: 1.15 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: 1.070 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.080 Find NCS groups from input model: 0.040 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- 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 3214 Z= 0.329 Angle : 0.895 15.004 4369 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 Details of bonding type rmsd hydrogen bonds : bond 0.13550 ( 202) hydrogen bonds : angle 5.47258 ( 609) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.44127 ( 4) covalent geometry : bond 0.00661 ( 3212) covalent geometry : angle 0.89554 ( 4365) *********************** 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 : 0.298 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: 0.7843 time to fit residues: 30.4805 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 : 0.331 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127864 restraints weight = 3025.519| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.15 r_work: 0.3317 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 3214 Z= 0.136 Angle : 0.586 7.962 4369 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 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 202) hydrogen bonds : angle 4.39132 ( 609) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.55430 ( 4) covalent geometry : bond 0.00298 ( 3212) covalent geometry : angle 0.58605 ( 4365) *********************** 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 : 0.335 Fit side-chains REVERT: N 35 ASP cc_start: 0.7471 (m-30) cc_final: 0.7268 (m-30) REVERT: N 98 ASN cc_start: 0.7543 (t0) cc_final: 0.6953 (t0) REVERT: R 231 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7523 (mmt) REVERT: R 281 LEU cc_start: 0.8201 (mm) cc_final: 0.8000 (mt) REVERT: R 290 ASP cc_start: 0.5840 (m-30) cc_final: 0.5348 (m-30) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.6892 time to fit residues: 25.6316 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 : 0.333 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.181125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123788 restraints weight = 3026.302| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.12 r_work: 0.3256 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3214 Z= 0.167 Angle : 0.614 7.366 4369 Z= 0.300 Chirality : 0.041 0.143 503 Planarity : 0.004 0.028 522 Dihedral : 13.133 137.287 589 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 0.36 (0.44), residues: 378 helix: 1.20 (0.35), residues: 229 sheet: 0.61 (0.77), residues: 54 loop : -2.40 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 38 HIS 0.004 0.001 HIS R 94 PHE 0.023 0.002 PHE R 207 TYR 0.013 0.001 TYR R 235 ARG 0.004 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.06088 ( 202) hydrogen bonds : angle 4.42643 ( 609) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.70424 ( 4) covalent geometry : bond 0.00390 ( 3212) covalent geometry : angle 0.61413 ( 4365) *********************** 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 40 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.305 Fit side-chains REVERT: N 98 ASN cc_start: 0.7824 (t0) cc_final: 0.7188 (t0) REVERT: R 231 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: R 281 LEU cc_start: 0.8270 (mm) cc_final: 0.8068 (mt) REVERT: R 303 ARG cc_start: 0.7171 (mmt180) cc_final: 0.6787 (mmp-170) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.8824 time to fit residues: 34.1218 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.181047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125409 restraints weight = 3051.011| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.04 r_work: 0.3282 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3214 Z= 0.140 Angle : 0.551 6.622 4369 Z= 0.273 Chirality : 0.039 0.136 503 Planarity : 0.004 0.030 522 Dihedral : 12.825 131.307 589 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 16.08 % Favored : 81.03 % 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: 0.67 (0.44), residues: 378 helix: 1.45 (0.35), residues: 227 sheet: 0.64 (0.76), residues: 54 loop : -2.13 (0.58), residues: 97 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 0.010 0.001 TYR N 34 ARG 0.003 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 202) hydrogen bonds : angle 4.26015 ( 609) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.61626 ( 4) covalent geometry : bond 0.00313 ( 3212) covalent geometry : angle 0.55074 ( 4365) *********************** 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 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.332 Fit side-chains REVERT: N 98 ASN cc_start: 0.7817 (t0) cc_final: 0.7160 (t0) REVERT: R 231 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7706 (mmt) REVERT: R 290 ASP cc_start: 0.5907 (m-30) cc_final: 0.5414 (m-30) REVERT: R 303 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6724 (mmp-170) outliers start: 9 outliers final: 4 residues processed: 36 average time/residue: 0.6985 time to fit residues: 26.6146 Evaluate side-chains 32 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 231 MET Chi-restraints excluded: chain R residue 239 LEU 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 5 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123629 restraints weight = 3059.887| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.12 r_work: 0.3259 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3214 Z= 0.148 Angle : 0.576 6.982 4369 Z= 0.282 Chirality : 0.039 0.143 503 Planarity : 0.004 0.031 522 Dihedral : 12.612 129.098 589 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 16.72 % 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: 0.55 (0.44), residues: 378 helix: 1.39 (0.34), residues: 229 sheet: 0.71 (0.76), residues: 54 loop : -2.44 (0.56), residues: 95 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 0.002 PHE R 207 TYR 0.011 0.001 TYR R 235 ARG 0.003 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.05628 ( 202) hydrogen bonds : angle 4.26958 ( 609) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.64153 ( 4) covalent geometry : bond 0.00336 ( 3212) covalent geometry : angle 0.57579 ( 4365) *********************** 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 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.359 Fit side-chains REVERT: N 98 ASN cc_start: 0.7846 (t0) cc_final: 0.7192 (t0) REVERT: R 231 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: R 290 ASP cc_start: 0.5831 (m-30) cc_final: 0.5358 (m-30) REVERT: R 303 ARG cc_start: 0.7266 (mmt180) cc_final: 0.6810 (mmp-170) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.7443 time to fit residues: 26.6817 Evaluate side-chains 33 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.182327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126600 restraints weight = 3134.759| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.07 r_work: 0.3285 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3214 Z= 0.124 Angle : 0.528 6.634 4369 Z= 0.261 Chirality : 0.038 0.136 503 Planarity : 0.003 0.032 522 Dihedral : 12.191 125.052 589 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.57 % Allowed : 18.01 % 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: 0.92 (0.44), residues: 378 helix: 1.69 (0.35), residues: 227 sheet: 0.76 (0.76), residues: 54 loop : -2.16 (0.59), 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 0.017 0.001 PHE R 207 TYR 0.009 0.001 TYR N 34 ARG 0.002 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 202) hydrogen bonds : angle 4.14921 ( 609) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.54342 ( 4) covalent geometry : bond 0.00264 ( 3212) covalent geometry : angle 0.52797 ( 4365) *********************** 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 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.343 Fit side-chains REVERT: N 98 ASN cc_start: 0.7800 (t0) cc_final: 0.7116 (t0) REVERT: R 231 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7541 (mmm) REVERT: R 290 ASP cc_start: 0.5769 (m-30) cc_final: 0.5305 (m-30) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.6094 time to fit residues: 22.8148 Evaluate side-chains 35 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.174724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119442 restraints weight = 3087.444| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.06 r_work: 0.3189 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3214 Z= 0.232 Angle : 0.700 8.556 4369 Z= 0.340 Chirality : 0.043 0.151 503 Planarity : 0.004 0.032 522 Dihedral : 12.754 131.725 589 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.86 % Allowed : 17.04 % 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: 0.16 (0.43), residues: 378 helix: 1.07 (0.33), residues: 231 sheet: 1.08 (0.85), residues: 45 loop : -2.67 (0.51), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 106 HIS 0.005 0.002 HIS R 94 PHE 0.022 0.002 PHE R 207 TYR 0.016 0.002 TYR R 235 ARG 0.006 0.001 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.07129 ( 202) hydrogen bonds : angle 4.53212 ( 609) SS BOND : bond 0.00459 ( 2) SS BOND : angle 0.89239 ( 4) covalent geometry : bond 0.00570 ( 3212) covalent geometry : angle 0.69942 ( 4365) *********************** 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 42 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.272 Fit side-chains REVERT: N 98 ASN cc_start: 0.7851 (t0) cc_final: 0.7149 (t0) REVERT: R 231 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7749 (mmt) REVERT: R 303 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6939 (mmp-170) outliers start: 12 outliers final: 9 residues processed: 36 average time/residue: 1.1620 time to fit residues: 43.8008 Evaluate side-chains 39 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 VAL 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 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.183057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128080 restraints weight = 3077.342| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.18 r_work: 0.3273 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3214 Z= 0.122 Angle : 0.548 7.372 4369 Z= 0.274 Chirality : 0.038 0.136 503 Planarity : 0.004 0.032 522 Dihedral : 12.197 124.432 589 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.57 % Allowed : 19.61 % 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: 0.80 (0.44), residues: 378 helix: 1.67 (0.34), residues: 227 sheet: 1.16 (0.83), residues: 45 loop : -2.39 (0.54), 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 94 PHE 0.021 0.002 PHE R 189 TYR 0.009 0.001 TYR N 34 ARG 0.002 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 202) hydrogen bonds : angle 4.20149 ( 609) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.64744 ( 4) covalent geometry : bond 0.00244 ( 3212) covalent geometry : angle 0.54812 ( 4365) *********************** 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 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.349 Fit side-chains REVERT: N 98 ASN cc_start: 0.7789 (t0) cc_final: 0.7171 (t0) REVERT: R 231 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (mmm) REVERT: R 290 ASP cc_start: 0.5781 (m-30) cc_final: 0.5306 (m-30) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.6384 time to fit residues: 25.0659 Evaluate side-chains 34 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain R residue 231 MET 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 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.180947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124938 restraints weight = 3045.756| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.07 r_work: 0.3275 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3214 Z= 0.124 Angle : 0.557 7.404 4369 Z= 0.272 Chirality : 0.038 0.130 503 Planarity : 0.004 0.032 522 Dihedral : 12.039 123.061 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.57 % Allowed : 19.29 % Favored : 78.14 % 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: 1.00 (0.44), residues: 378 helix: 1.85 (0.34), residues: 227 sheet: 1.23 (0.83), residues: 45 loop : -2.36 (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 0.015 0.002 PHE R 207 TYR 0.009 0.001 TYR R 235 ARG 0.002 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 202) hydrogen bonds : angle 4.13816 ( 609) SS BOND : bond 0.00342 ( 2) SS BOND : angle 0.48155 ( 4) covalent geometry : bond 0.00261 ( 3212) covalent geometry : angle 0.55750 ( 4365) *********************** 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 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.342 Fit side-chains REVERT: N 98 ASN cc_start: 0.7802 (t0) cc_final: 0.7143 (t0) REVERT: R 231 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7528 (mmm) REVERT: R 290 ASP cc_start: 0.5781 (m-30) cc_final: 0.5322 (m-30) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.7935 time to fit residues: 30.0253 Evaluate side-chains 34 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.0030 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126022 restraints weight = 3033.194| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.10 r_work: 0.3305 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3214 Z= 0.118 Angle : 0.546 8.054 4369 Z= 0.263 Chirality : 0.038 0.132 503 Planarity : 0.003 0.032 522 Dihedral : 11.749 120.392 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: 1.12 (0.44), residues: 378 helix: 1.92 (0.34), residues: 227 sheet: 0.77 (0.74), residues: 54 loop : -2.25 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 338 HIS 0.002 0.001 HIS R 202 PHE 0.014 0.002 PHE R 189 TYR 0.008 0.001 TYR N 34 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 202) hydrogen bonds : angle 4.07827 ( 609) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.46851 ( 4) covalent geometry : bond 0.00241 ( 3212) covalent geometry : angle 0.54572 ( 4365) ********************** 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 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.328 Fit side-chains REVERT: N 98 ASN cc_start: 0.7831 (t0) cc_final: 0.7148 (t0) REVERT: R 231 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7562 (mmm) REVERT: R 290 ASP cc_start: 0.5840 (m-30) cc_final: 0.5369 (m-30) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.6273 time to fit residues: 23.3530 Evaluate side-chains 34 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.180264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124019 restraints weight = 3082.960| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.10 r_work: 0.3265 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3214 Z= 0.132 Angle : 0.567 7.595 4369 Z= 0.275 Chirality : 0.039 0.132 503 Planarity : 0.004 0.032 522 Dihedral : 11.779 120.332 589 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 1.00 (0.44), residues: 378 helix: 1.85 (0.34), residues: 227 sheet: 1.23 (0.83), residues: 45 loop : -2.38 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 PHE 0.024 0.001 PHE R 189 TYR 0.010 0.001 TYR R 235 ARG 0.002 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 202) hydrogen bonds : angle 4.11914 ( 609) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.47550 ( 4) covalent geometry : bond 0.00286 ( 3212) covalent geometry : angle 0.56714 ( 4365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.21 seconds wall clock time: 43 minutes 51.28 seconds (2631.28 seconds total)