Starting phenix.real_space_refine on Wed Sep 17 11:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdh_38278/09_2025/8xdh_38278.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.211 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5511 2.51 5 N 1344 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2750 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 343} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 20 Number of conformers: 3 Conformer: "B" Number of residues, atoms: 2, 8 Unusual residues: {'URE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "A" Number of residues, atoms: 2, 8 Unusual residues: {'URE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "C" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" C BURE A 501 " occ=0.25 ... (2 atoms not shown) pdb=" N2 BURE A 501 " occ=0.25 residue: pdb=" C AURE A 502 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE A 502 " occ=0.25 residue: pdb=" C CURE A 503 " occ=0.50 ... (2 atoms not shown) pdb=" N2 CURE A 503 " occ=0.50 residue: pdb=" C AURE A 504 " occ=0.50 ... (2 atoms not shown) pdb=" N2 AURE A 504 " occ=0.50 residue: pdb=" C BURE A 505 " occ=0.50 ... (2 atoms not shown) pdb=" N2 BURE A 505 " occ=0.50 residue: pdb=" C BURE B 501 " occ=0.25 ... (2 atoms not shown) pdb=" N2 BURE B 501 " occ=0.25 residue: pdb=" C AURE B 502 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE B 502 " occ=0.25 residue: pdb=" C CURE B 503 " occ=0.50 ... (2 atoms not shown) pdb=" N2 CURE B 503 " occ=0.50 residue: pdb=" C AURE B 504 " occ=0.50 ... (2 atoms not shown) pdb=" N2 AURE B 504 " occ=0.50 residue: pdb=" C BURE B 505 " occ=0.50 ... (2 atoms not shown) pdb=" N2 BURE B 505 " occ=0.50 residue: pdb=" C BURE C 501 " occ=0.25 ... (2 atoms not shown) pdb=" N2 BURE C 501 " occ=0.25 residue: pdb=" C AURE C 502 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE C 502 " occ=0.25 ... (remaining 3 not shown) Time building chain proxies: 2.27, per 1000 atoms: 0.27 Number of scatterers: 8310 At special positions: 0 Unit cell: (105.8, 103.96, 76.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1383 8.00 N 1344 7.00 C 5511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 441.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 168 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.730A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 304 through 330 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.619A pdb=" N ILE A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 368 through 385 Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 168 Proline residue: B 157 - end of helix Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 231 removed outlier: 4.729A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 226 - end of helix Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 237 through 252 Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 304 through 330 Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.620A pdb=" N ILE B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 368 through 385 Processing helix chain 'C' and resid 29 through 38 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 168 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 231 removed outlier: 4.729A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 237 through 252 Processing helix chain 'C' and resid 252 through 273 Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 304 through 330 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.621A pdb=" N ILE C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 368 through 385 571 hydrogen bonds defined for protein. 1677 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: 1.30 Time building geometry restraints manager: 1.05 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: 1233 1.31 - 1.43: 2566 1.43 - 1.56: 4640 1.56 - 1.68: 0 1.68 - 1.81: 114 Bond restraints: 8553 Sorted by residual: bond pdb=" CA PHE B 175 " pdb=" C PHE B 175 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.12e-02 7.97e+03 2.54e+01 bond pdb=" CA PHE A 175 " pdb=" C PHE A 175 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.12e-02 7.97e+03 2.53e+01 bond pdb=" CA PHE C 175 " pdb=" C PHE C 175 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.12e-02 7.97e+03 2.49e+01 bond pdb=" C AURE C 504 " pdb=" N1 AURE C 504 " ideal model delta sigma weight residual 1.363 1.454 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C AURE C 502 " pdb=" N2 AURE C 502 " ideal model delta sigma weight residual 1.363 1.454 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 8548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 11232 2.14 - 4.27: 337 4.27 - 6.41: 74 6.41 - 8.54: 24 8.54 - 10.68: 9 Bond angle restraints: 11676 Sorted by residual: angle pdb=" N VAL C 232 " pdb=" CA VAL C 232 " pdb=" C VAL C 232 " ideal model delta sigma weight residual 110.72 103.42 7.30 1.01e+00 9.80e-01 5.22e+01 angle pdb=" N VAL B 232 " pdb=" CA VAL B 232 " pdb=" C VAL B 232 " ideal model delta sigma weight residual 110.72 103.46 7.26 1.01e+00 9.80e-01 5.17e+01 angle pdb=" N VAL A 232 " pdb=" CA VAL A 232 " pdb=" C VAL A 232 " ideal model delta sigma weight residual 110.72 103.46 7.26 1.01e+00 9.80e-01 5.17e+01 angle pdb=" N CYS C 337 " pdb=" CA CYS C 337 " pdb=" C CYS C 337 " ideal model delta sigma weight residual 111.07 117.43 -6.36 1.07e+00 8.73e-01 3.53e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 111.07 117.40 -6.33 1.07e+00 8.73e-01 3.50e+01 ... (remaining 11671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 4110 11.92 - 23.85: 445 23.85 - 35.77: 164 35.77 - 47.69: 36 47.69 - 59.61: 18 Dihedral angle restraints: 4773 sinusoidal: 1692 harmonic: 3081 Sorted by residual: dihedral pdb=" CA GLY A 114 " pdb=" C GLY A 114 " pdb=" N ALA A 115 " pdb=" CA ALA A 115 " ideal model delta harmonic sigma weight residual 180.00 164.61 15.39 0 5.00e+00 4.00e-02 9.47e+00 dihedral pdb=" CA GLY B 114 " pdb=" C GLY B 114 " pdb=" N ALA B 115 " pdb=" CA ALA B 115 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" CA GLY C 114 " pdb=" C GLY C 114 " pdb=" N ALA C 115 " pdb=" CA ALA C 115 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 4770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1137 0.073 - 0.146: 133 0.146 - 0.219: 24 0.219 - 0.292: 14 0.292 - 0.365: 9 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA TRP C 33 " pdb=" N TRP C 33 " pdb=" C TRP C 33 " pdb=" CB TRP C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA TRP B 33 " pdb=" N TRP B 33 " pdb=" C TRP B 33 " pdb=" CB TRP B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA TRP A 33 " pdb=" N TRP A 33 " pdb=" C TRP A 33 " pdb=" CB TRP A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1314 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 334 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO C 335 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 334 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 335 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 334 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO B 335 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.031 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2621 2.82 - 3.34: 8536 3.34 - 3.86: 14636 3.86 - 4.38: 17523 4.38 - 4.90: 28852 Nonbonded interactions: 72168 Sorted by model distance: nonbonded pdb=" O ALA C 367 " pdb=" ND2 ASN C 372 " model vdw 2.304 3.120 nonbonded pdb=" O ALA B 367 " pdb=" ND2 ASN B 372 " model vdw 2.304 3.120 nonbonded pdb=" O ALA A 367 " pdb=" ND2 ASN A 372 " model vdw 2.304 3.120 nonbonded pdb=" O TRP B 47 " pdb=" NE2 GLN B 51 " model vdw 2.309 3.120 nonbonded pdb=" O TRP A 47 " pdb=" NE2 GLN A 51 " model vdw 2.309 3.120 ... (remaining 72163 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.25 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.010 0.091 8553 Z= 0.554 Angle : 0.938 10.681 11676 Z= 0.554 Chirality : 0.064 0.365 1317 Planarity : 0.005 0.052 1431 Dihedral : 12.346 59.613 2805 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1068 helix: 0.99 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 0.23 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 89 TYR 0.025 0.003 TYR C 320 PHE 0.031 0.002 PHE B 179 TRP 0.023 0.002 TRP B 33 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00978 ( 8553) covalent geometry : angle 0.93845 (11676) hydrogen bonds : bond 0.12408 ( 571) hydrogen bonds : angle 6.06257 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.293 Fit side-chains REVERT: A 41 MET cc_start: 0.8203 (mtp) cc_final: 0.7843 (mtm) REVERT: A 176 THR cc_start: 0.7563 (m) cc_final: 0.7296 (p) REVERT: A 327 ASN cc_start: 0.8042 (m-40) cc_final: 0.7735 (m110) REVERT: A 365 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7646 (mmmt) REVERT: B 41 MET cc_start: 0.8247 (mtp) cc_final: 0.7926 (mtm) REVERT: B 224 SER cc_start: 0.7183 (t) cc_final: 0.6864 (m) REVERT: B 365 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7566 (mmmt) REVERT: C 40 ASP cc_start: 0.7654 (m-30) cc_final: 0.7415 (m-30) REVERT: C 41 MET cc_start: 0.8082 (mtp) cc_final: 0.7830 (mtp) REVERT: C 176 THR cc_start: 0.7786 (m) cc_final: 0.7390 (p) REVERT: C 224 SER cc_start: 0.7008 (t) cc_final: 0.6751 (m) REVERT: C 365 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7526 (mmmt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0695 time to fit residues: 12.5262 Evaluate side-chains 96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN B 327 ASN C 94 ASN C 180 ASN C 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.104656 restraints weight = 8957.046| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 0.72 r_work: 0.2856 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8553 Z= 0.147 Angle : 0.563 6.001 11676 Z= 0.297 Chirality : 0.039 0.121 1317 Planarity : 0.004 0.027 1431 Dihedral : 4.335 14.955 1131 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.19 % Allowed : 7.17 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.27), residues: 1068 helix: 1.42 (0.19), residues: 789 sheet: None (None), residues: 0 loop : 0.16 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.020 0.001 TYR B 320 PHE 0.012 0.001 PHE B 341 TRP 0.009 0.001 TRP B 90 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8553) covalent geometry : angle 0.56342 (11676) hydrogen bonds : bond 0.04205 ( 571) hydrogen bonds : angle 4.30604 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.233 Fit side-chains REVERT: A 41 MET cc_start: 0.8683 (mtp) cc_final: 0.8393 (mtp) REVERT: A 365 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8315 (mmmt) REVERT: B 41 MET cc_start: 0.8714 (mtp) cc_final: 0.8257 (mtp) REVERT: B 224 SER cc_start: 0.8724 (t) cc_final: 0.8438 (m) REVERT: B 267 MET cc_start: 0.8512 (ptm) cc_final: 0.8214 (ptm) REVERT: B 365 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8240 (mmmt) REVERT: C 199 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8326 (mm-40) REVERT: C 208 MET cc_start: 0.7853 (tpp) cc_final: 0.7630 (tpt) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.0676 time to fit residues: 10.7242 Evaluate side-chains 92 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 331 ASN B 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.094926 restraints weight = 9133.088| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 0.84 r_work: 0.2723 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8553 Z= 0.152 Angle : 0.549 6.024 11676 Z= 0.288 Chirality : 0.039 0.122 1317 Planarity : 0.004 0.031 1431 Dihedral : 4.296 14.764 1131 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.91 % Allowed : 8.96 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.26), residues: 1068 helix: 1.55 (0.19), residues: 786 sheet: None (None), residues: 0 loop : 0.23 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 63 TYR 0.016 0.001 TYR C 320 PHE 0.016 0.001 PHE B 341 TRP 0.008 0.001 TRP B 90 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8553) covalent geometry : angle 0.54855 (11676) hydrogen bonds : bond 0.04199 ( 571) hydrogen bonds : angle 4.25769 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.310 Fit side-chains REVERT: A 41 MET cc_start: 0.8761 (mtp) cc_final: 0.8494 (mtp) REVERT: A 154 MET cc_start: 0.9109 (mtp) cc_final: 0.8750 (mtp) REVERT: A 365 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8280 (mmmt) REVERT: B 41 MET cc_start: 0.8717 (mtp) cc_final: 0.8308 (mtp) REVERT: B 224 SER cc_start: 0.8748 (t) cc_final: 0.8521 (m) REVERT: B 267 MET cc_start: 0.8475 (ptm) cc_final: 0.8110 (ptm) REVERT: B 355 THR cc_start: 0.8099 (t) cc_final: 0.7834 (t) REVERT: B 365 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8162 (mmmt) REVERT: C 41 MET cc_start: 0.8406 (mtp) cc_final: 0.8197 (mtp) outliers start: 16 outliers final: 15 residues processed: 93 average time/residue: 0.0673 time to fit residues: 9.6644 Evaluate side-chains 97 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.111095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.095628 restraints weight = 9260.640| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 0.85 r_work: 0.2760 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8553 Z= 0.135 Angle : 0.518 5.953 11676 Z= 0.272 Chirality : 0.038 0.122 1317 Planarity : 0.004 0.030 1431 Dihedral : 4.187 14.242 1131 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.03 % Allowed : 9.08 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.26), residues: 1068 helix: 1.70 (0.19), residues: 786 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.013 0.001 TYR C 368 PHE 0.014 0.001 PHE B 341 TRP 0.008 0.001 TRP B 90 HIS 0.002 0.000 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8553) covalent geometry : angle 0.51752 (11676) hydrogen bonds : bond 0.04012 ( 571) hydrogen bonds : angle 4.11228 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.312 Fit side-chains REVERT: A 41 MET cc_start: 0.8727 (mtp) cc_final: 0.8432 (mtp) REVERT: A 154 MET cc_start: 0.9072 (mtp) cc_final: 0.8728 (mtp) REVERT: A 365 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8198 (mmmt) REVERT: B 41 MET cc_start: 0.8646 (mtp) cc_final: 0.8212 (mtp) REVERT: B 224 SER cc_start: 0.8728 (t) cc_final: 0.8519 (m) REVERT: B 267 MET cc_start: 0.8407 (ptm) cc_final: 0.8022 (ptm) REVERT: B 365 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8147 (mmmt) REVERT: C 41 MET cc_start: 0.8329 (mtp) cc_final: 0.8114 (mtp) outliers start: 17 outliers final: 15 residues processed: 96 average time/residue: 0.0872 time to fit residues: 11.9790 Evaluate side-chains 98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.107399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.091780 restraints weight = 9190.558| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 0.81 r_work: 0.2749 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8553 Z= 0.170 Angle : 0.553 6.051 11676 Z= 0.291 Chirality : 0.039 0.126 1317 Planarity : 0.004 0.033 1431 Dihedral : 4.309 15.165 1131 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 9.68 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.27), residues: 1068 helix: 1.64 (0.19), residues: 783 sheet: None (None), residues: 0 loop : 0.40 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 63 TYR 0.017 0.001 TYR B 368 PHE 0.016 0.001 PHE B 341 TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8553) covalent geometry : angle 0.55295 (11676) hydrogen bonds : bond 0.04275 ( 571) hydrogen bonds : angle 4.22746 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.428 Fit side-chains REVERT: A 41 MET cc_start: 0.8804 (mtp) cc_final: 0.8462 (mtp) REVERT: A 47 TRP cc_start: 0.8652 (t60) cc_final: 0.8412 (t60) REVERT: A 154 MET cc_start: 0.9227 (mtp) cc_final: 0.8959 (mtp) REVERT: A 365 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8024 (mmmt) REVERT: B 41 MET cc_start: 0.8798 (mtp) cc_final: 0.8293 (mtp) REVERT: B 154 MET cc_start: 0.9066 (mtp) cc_final: 0.8827 (mtt) REVERT: B 224 SER cc_start: 0.8623 (t) cc_final: 0.8393 (p) REVERT: B 365 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8134 (mmmt) outliers start: 20 outliers final: 17 residues processed: 98 average time/residue: 0.0750 time to fit residues: 11.4133 Evaluate side-chains 104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 379 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.110643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.095667 restraints weight = 9113.310| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 0.77 r_work: 0.2766 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8553 Z= 0.151 Angle : 0.527 6.012 11676 Z= 0.278 Chirality : 0.039 0.124 1317 Planarity : 0.004 0.033 1431 Dihedral : 4.259 15.819 1131 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.39 % Allowed : 10.27 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.27), residues: 1068 helix: 1.70 (0.19), residues: 783 sheet: None (None), residues: 0 loop : 0.38 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.014 0.001 TYR B 368 PHE 0.012 0.001 PHE B 341 TRP 0.008 0.001 TRP B 90 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8553) covalent geometry : angle 0.52746 (11676) hydrogen bonds : bond 0.04105 ( 571) hydrogen bonds : angle 4.17362 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.307 Fit side-chains REVERT: A 41 MET cc_start: 0.8814 (mtp) cc_final: 0.8481 (mtp) REVERT: A 47 TRP cc_start: 0.8675 (t60) cc_final: 0.8472 (t60) REVERT: A 154 MET cc_start: 0.9197 (mtp) cc_final: 0.8930 (mtp) REVERT: A 365 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8060 (mmmt) REVERT: B 224 SER cc_start: 0.8651 (t) cc_final: 0.8421 (p) REVERT: B 267 MET cc_start: 0.8384 (ptm) cc_final: 0.8084 (ptm) REVERT: B 355 THR cc_start: 0.8082 (t) cc_final: 0.7801 (t) REVERT: B 365 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8161 (mmmt) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.0735 time to fit residues: 11.4328 Evaluate side-chains 106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 379 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.095931 restraints weight = 9187.892| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 0.78 r_work: 0.2761 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8553 Z= 0.146 Angle : 0.516 6.006 11676 Z= 0.272 Chirality : 0.039 0.124 1317 Planarity : 0.004 0.033 1431 Dihedral : 4.237 18.985 1131 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.27 % Allowed : 10.99 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.27), residues: 1068 helix: 1.73 (0.19), residues: 783 sheet: None (None), residues: 0 loop : 0.42 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.014 0.001 TYR B 368 PHE 0.015 0.001 PHE B 341 TRP 0.008 0.001 TRP B 90 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8553) covalent geometry : angle 0.51643 (11676) hydrogen bonds : bond 0.04073 ( 571) hydrogen bonds : angle 4.15519 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.295 Fit side-chains REVERT: A 41 MET cc_start: 0.8817 (mtp) cc_final: 0.8499 (mtp) REVERT: A 154 MET cc_start: 0.9173 (mtp) cc_final: 0.8913 (mtp) REVERT: A 365 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8074 (mmmt) REVERT: B 224 SER cc_start: 0.8622 (t) cc_final: 0.8399 (p) REVERT: B 267 MET cc_start: 0.8382 (ptm) cc_final: 0.8068 (ptm) REVERT: B 365 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8187 (mmmt) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0687 time to fit residues: 10.2159 Evaluate side-chains 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.106161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.091831 restraints weight = 9199.612| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 0.76 r_work: 0.2633 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8553 Z= 0.157 Angle : 0.528 6.021 11676 Z= 0.277 Chirality : 0.039 0.125 1317 Planarity : 0.004 0.033 1431 Dihedral : 4.272 18.629 1131 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.15 % Allowed : 11.35 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.27), residues: 1068 helix: 1.70 (0.19), residues: 783 sheet: None (None), residues: 0 loop : 0.47 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.015 0.001 TYR B 368 PHE 0.015 0.001 PHE B 341 TRP 0.008 0.001 TRP B 90 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8553) covalent geometry : angle 0.52785 (11676) hydrogen bonds : bond 0.04149 ( 571) hydrogen bonds : angle 4.18890 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.318 Fit side-chains REVERT: A 41 MET cc_start: 0.8747 (mtp) cc_final: 0.8422 (mtp) REVERT: A 154 MET cc_start: 0.9249 (mtp) cc_final: 0.9029 (mtp) REVERT: A 365 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8142 (mmmt) REVERT: B 224 SER cc_start: 0.8710 (t) cc_final: 0.8488 (p) REVERT: B 267 MET cc_start: 0.8515 (ptm) cc_final: 0.8199 (ptm) REVERT: B 365 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8280 (mmmt) REVERT: C 40 ASP cc_start: 0.8314 (m-30) cc_final: 0.8015 (m-30) outliers start: 18 outliers final: 17 residues processed: 98 average time/residue: 0.0702 time to fit residues: 10.6313 Evaluate side-chains 103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 74 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.094130 restraints weight = 9169.268| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 0.79 r_work: 0.2775 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8553 Z= 0.136 Angle : 0.506 5.980 11676 Z= 0.266 Chirality : 0.038 0.151 1317 Planarity : 0.004 0.032 1431 Dihedral : 4.162 16.454 1131 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.03 % Allowed : 11.83 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1068 helix: 1.93 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.012 0.001 TYR B 368 PHE 0.013 0.001 PHE B 341 TRP 0.013 0.001 TRP A 47 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8553) covalent geometry : angle 0.50592 (11676) hydrogen bonds : bond 0.03991 ( 571) hydrogen bonds : angle 4.10385 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.304 Fit side-chains REVERT: A 41 MET cc_start: 0.8800 (mtp) cc_final: 0.8446 (mtp) REVERT: A 365 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8072 (mmmt) REVERT: B 224 SER cc_start: 0.8619 (t) cc_final: 0.8397 (p) REVERT: B 267 MET cc_start: 0.8354 (ptm) cc_final: 0.8038 (ptm) REVERT: B 355 THR cc_start: 0.8075 (t) cc_final: 0.7787 (t) REVERT: B 365 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8220 (mmmt) REVERT: C 40 ASP cc_start: 0.7970 (m-30) cc_final: 0.7625 (m-30) outliers start: 17 outliers final: 16 residues processed: 95 average time/residue: 0.0731 time to fit residues: 10.6777 Evaluate side-chains 103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 68 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 92 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 0.0000 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.100669 restraints weight = 9124.129| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 0.78 r_work: 0.2833 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8553 Z= 0.109 Angle : 0.468 5.912 11676 Z= 0.246 Chirality : 0.037 0.146 1317 Planarity : 0.003 0.031 1431 Dihedral : 3.860 13.023 1131 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 12.90 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.26), residues: 1068 helix: 2.09 (0.19), residues: 777 sheet: None (None), residues: 0 loop : 0.11 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.010 0.001 TYR A 301 PHE 0.009 0.001 PHE B 341 TRP 0.013 0.001 TRP C 339 HIS 0.001 0.000 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8553) covalent geometry : angle 0.46803 (11676) hydrogen bonds : bond 0.03665 ( 571) hydrogen bonds : angle 3.88596 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.329 Fit side-chains REVERT: A 38 SER cc_start: 0.8508 (p) cc_final: 0.8287 (m) REVERT: A 41 MET cc_start: 0.8641 (mtp) cc_final: 0.8314 (mtp) REVERT: A 327 ASN cc_start: 0.9151 (m110) cc_final: 0.8849 (m110) REVERT: A 365 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8035 (mmmt) REVERT: B 224 SER cc_start: 0.8636 (t) cc_final: 0.8390 (p) REVERT: B 267 MET cc_start: 0.8164 (ptm) cc_final: 0.7834 (ptm) REVERT: B 365 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8149 (mmmt) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.0709 time to fit residues: 11.4370 Evaluate side-chains 105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.108448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.092833 restraints weight = 9224.724| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 0.81 r_work: 0.2757 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8553 Z= 0.154 Angle : 0.526 6.047 11676 Z= 0.274 Chirality : 0.039 0.155 1317 Planarity : 0.004 0.032 1431 Dihedral : 4.122 15.470 1131 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.96 % Allowed : 13.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.27), residues: 1068 helix: 1.87 (0.19), residues: 786 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.016 0.001 TYR B 368 PHE 0.026 0.001 PHE B 36 TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8553) covalent geometry : angle 0.52566 (11676) hydrogen bonds : bond 0.04095 ( 571) hydrogen bonds : angle 4.09753 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.39 seconds wall clock time: 37 minutes 20.90 seconds (2240.90 seconds total)