Starting phenix.real_space_refine on Tue Mar 3 12:29:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.cif Found real_map, /net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.map" model { file = "/net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28qn_56751/03_2026/28qn_56751.cif" } resolution = 3.3 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= 0.000 sd= 0.006 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 9 5.16 5 C 2614 2.51 5 N 682 2.21 5 O 782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4087 Number of models: 1 Model: "" Number of chains: 4 Chain: "Ba" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2908 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 21, 'TRANS': 352} Chain: "A" Number of atoms: 1153 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 1145 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 155} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 160, 1145 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 155} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 1158 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'EOH': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 29 " occ=0.98 ... (8 atoms not shown) pdb=" CB BGLU A 29 " occ=0.02 Time building chain proxies: 1.23, per 1000 atoms: 0.30 Number of scatterers: 4087 At special positions: 0 Unit cell: (71.294, 96.164, 74.61, 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 9 16.00 O 782 8.00 N 682 7.00 C 2614 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 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 208.5 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 56.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'Ba' and resid 17 through 32 Processing helix chain 'Ba' and resid 43 through 55 Proline residue: Ba 49 - end of helix removed outlier: 4.420A pdb=" N THRBa 54 " --> pdb=" O GLNBa 50 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 67 through 74 removed outlier: 3.565A pdb=" N SERBa 74 " --> pdb=" O GLYBa 70 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 83 through 90 removed outlier: 3.509A pdb=" N LYSBa 89 " --> pdb=" O ALABa 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEUBa 90 " --> pdb=" O PHEBa 86 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 91 through 97 removed outlier: 3.601A pdb=" N TRPBa 95 " --> pdb=" O TYRBa 91 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASPBa 96 " --> pdb=" O PROBa 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALABa 97 " --> pdb=" O PHEBa 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 91 through 97' Processing helix chain 'Ba' and resid 131 through 143 removed outlier: 4.572A pdb=" N ALABa 135 " --> pdb=" O GLUBa 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYSBa 143 " --> pdb=" O GLUBa 139 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 154 through 164 removed outlier: 3.724A pdb=" N THRBa 158 " --> pdb=" O GLUBa 154 " (cutoff:3.500A) Proline residue: Ba 160 - end of helix Processing helix chain 'Ba' and resid 186 through 202 Processing helix chain 'Ba' and resid 210 through 220 Processing helix chain 'Ba' and resid 229 through 231 No H-bonds generated for 'chain 'Ba' and resid 229 through 231' Processing helix chain 'Ba' and resid 232 through 240 removed outlier: 3.560A pdb=" N ILEBa 236 " --> pdb=" O ALABa 232 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 273 through 284 Processing helix chain 'Ba' and resid 287 through 298 removed outlier: 3.772A pdb=" N ALABa 293 " --> pdb=" O GLUBa 289 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VALBa 294 " --> pdb=" O GLYBa 290 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 305 through 313 removed outlier: 3.891A pdb=" N GLUBa 311 " --> pdb=" O SERBa 307 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 315 through 328 Processing helix chain 'Ba' and resid 336 through 354 removed outlier: 3.824A pdb=" N TYRBa 342 " --> pdb=" O SERBa 338 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 357 through 371 removed outlier: 3.744A pdb=" N HISBa 371 " --> pdb=" O THRBa 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 removed outlier: 4.141A pdb=" N LEU A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.612A pdb=" N MET A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 158 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.968A pdb=" N ARG A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ba' and resid 36 through 39 removed outlier: 6.547A pdb=" N VALBa 9 " --> pdb=" O ILEBa 60 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHEBa 62 " --> pdb=" O VALBa 9 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRPBa 11 " --> pdb=" O PHEBa 62 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ALABa 64 " --> pdb=" O TRPBa 11 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALABa 265 " --> pdb=" O PROBa 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ba' and resid 36 through 39 removed outlier: 6.547A pdb=" N VALBa 9 " --> pdb=" O ILEBa 60 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHEBa 62 " --> pdb=" O VALBa 9 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRPBa 11 " --> pdb=" O PHEBa 62 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ALABa 64 " --> pdb=" O TRPBa 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ba' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'Ba' and resid 146 through 148 removed outlier: 6.520A pdb=" N ALABa 147 " --> pdb=" O METBa 225 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILEBa 227 " --> pdb=" O ALABa 147 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALABa 224 " --> pdb=" O ASNBa 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ba' and resid 171 through 172 removed outlier: 3.929A pdb=" N LYSBa 171 " --> pdb=" O ASPBa 178 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 581 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: 0.53 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1333 1.34 - 1.46: 696 1.46 - 1.57: 2137 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 4184 Sorted by residual: bond pdb=" N VAL A 30 " pdb=" CA VAL A 30 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.72e+00 bond pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.19e-02 7.06e+03 6.30e+00 bond pdb=" N LEU A 19 " pdb=" CA LEU A 19 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.13e+00 bond pdb=" N TYR A 89 " pdb=" CA TYR A 89 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.04e+00 bond pdb=" N GLU A 20 " pdb=" CA GLU A 20 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.96e+00 ... (remaining 4179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 5388 1.08 - 2.16: 200 2.16 - 3.24: 82 3.24 - 4.32: 16 4.32 - 5.40: 6 Bond angle restraints: 5692 Sorted by residual: angle pdb=" CA ASP A 28 " pdb=" C ASP A 28 " pdb=" O ASP A 28 " ideal model delta sigma weight residual 122.63 117.23 5.40 1.29e+00 6.01e-01 1.75e+01 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 112.90 108.80 4.10 1.31e+00 5.83e-01 9.79e+00 angle pdb=" N ILE A 32 " pdb=" CA ILE A 32 " pdb=" C ILE A 32 " ideal model delta sigma weight residual 111.17 107.23 3.94 1.38e+00 5.25e-01 8.13e+00 angle pdb=" CA LYS A 17 " pdb=" C LYS A 17 " pdb=" O LYS A 17 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.36e+00 angle pdb=" CA LEU A 19 " pdb=" C LEU A 19 " pdb=" O LEU A 19 " ideal model delta sigma weight residual 120.90 118.01 2.89 1.07e+00 8.73e-01 7.29e+00 ... (remaining 5687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 2154 16.85 - 33.70: 258 33.70 - 50.55: 72 50.55 - 67.40: 12 67.40 - 84.25: 3 Dihedral angle restraints: 2499 sinusoidal: 961 harmonic: 1538 Sorted by residual: dihedral pdb=" CA GLUBa 46 " pdb=" CB GLUBa 46 " pdb=" CG GLUBa 46 " pdb=" CD GLUBa 46 " ideal model delta sinusoidal sigma weight residual 180.00 120.54 59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYSBa 16 " pdb=" CD LYSBa 16 " pdb=" CE LYSBa 16 " pdb=" NZ LYSBa 16 " ideal model delta sinusoidal sigma weight residual -180.00 -121.45 -58.55 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSBa 171 " pdb=" CB LYSBa 171 " pdb=" CG LYSBa 171 " pdb=" CD LYSBa 171 " ideal model delta sinusoidal sigma weight residual -180.00 -122.87 -57.13 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 560 0.067 - 0.133: 67 0.133 - 0.200: 4 0.200 - 0.266: 1 0.266 - 0.333: 1 Chirality restraints: 633 Sorted by residual: chirality pdb=" C1 GLC B 2 " pdb=" O4 GLC B 1 " pdb=" C2 GLC B 2 " pdb=" O5 GLC B 2 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 GLC B 1 " pdb=" C2 GLC B 1 " pdb=" O1 GLC B 1 " pdb=" O5 GLC B 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.37 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ILE A 32 " pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CB ILE A 32 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 630 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 28 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C ASP A 28 " -0.096 2.00e-02 2.50e+03 pdb=" O ASP A 28 " 0.036 2.00e-02 2.50e+03 pdb=" N AGLU A 29 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 28 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C ASP A 28 " -0.096 2.00e-02 2.50e+03 pdb=" O ASP A 28 " 0.036 2.00e-02 2.50e+03 pdb=" N BGLU A 29 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AGLU A 29 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C AGLU A 29 " -0.087 2.00e-02 2.50e+03 pdb=" O AGLU A 29 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL A 30 " 0.030 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 49 2.67 - 3.23: 3975 3.23 - 3.78: 6386 3.78 - 4.34: 8724 4.34 - 4.90: 14471 Nonbonded interactions: 33605 Sorted by model distance: nonbonded pdb=" OE2 GLUBa 112 " pdb=" O2 GLC B 1 " model vdw 2.112 3.040 nonbonded pdb=" OE1 GLUBa 154 " pdb=" O6 GLC B 2 " model vdw 2.210 3.040 nonbonded pdb=" OG SERBa 271 " pdb=" OD1 ASNBa 273 " model vdw 2.280 3.040 nonbonded pdb=" NE2 HISBa 65 " pdb=" O METBa 331 " model vdw 2.281 3.120 nonbonded pdb=" OD2 ASPBa 31 " pdb=" OH TYRBa 284 " model vdw 2.326 3.040 ... (remaining 33600 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=0.02 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.930 Find NCS groups from input model: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.003 0.040 4185 Z= 0.217 Angle : 0.587 5.399 5695 Z= 0.351 Chirality : 0.045 0.333 633 Planarity : 0.006 0.055 737 Dihedral : 15.854 84.251 1517 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.96 % Favored : 95.85 % Rotamer: Outliers : 0.74 % Allowed : 25.31 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.36), residues: 534 helix: 0.97 (0.31), residues: 262 sheet: 0.58 (0.79), residues: 38 loop : -0.98 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 154 TYR 0.012 0.001 TYR A 89 PHE 0.006 0.001 PHEBa 62 TRP 0.009 0.001 TRPBa 159 HIS 0.015 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4184) covalent geometry : angle 0.58494 ( 5692) hydrogen bonds : bond 0.14543 ( 189) hydrogen bonds : angle 6.57655 ( 581) link_ALPHA1-4 : bond 0.00577 ( 1) link_ALPHA1-4 : angle 2.26858 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.144 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.0725 time to fit residues: 6.5253 Evaluate side-chains 66 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain A residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 186 ASN Ba 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121625 restraints weight = 8007.399| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.47 r_work: 0.3381 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4185 Z= 0.123 Angle : 0.500 5.144 5695 Z= 0.259 Chirality : 0.040 0.127 633 Planarity : 0.004 0.045 737 Dihedral : 4.341 47.105 609 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.53 % Favored : 95.28 % Rotamer: Outliers : 2.98 % Allowed : 25.31 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.36), residues: 534 helix: 1.29 (0.31), residues: 261 sheet: 0.51 (0.80), residues: 38 loop : -0.74 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 317 TYR 0.008 0.001 TYRBa 118 PHE 0.010 0.001 PHEBa 28 TRP 0.006 0.001 TRP A 123 HIS 0.016 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4184) covalent geometry : angle 0.49836 ( 5692) hydrogen bonds : bond 0.03890 ( 189) hydrogen bonds : angle 5.11520 ( 581) link_ALPHA1-4 : bond 0.00808 ( 1) link_ALPHA1-4 : angle 1.81671 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.184 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.0787 time to fit residues: 7.1497 Evaluate side-chains 69 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123406 restraints weight = 8564.040| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.81 r_work: 0.3359 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4185 Z= 0.136 Angle : 0.503 5.368 5695 Z= 0.259 Chirality : 0.040 0.128 633 Planarity : 0.004 0.048 737 Dihedral : 4.174 47.149 607 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.96 % Favored : 95.85 % Rotamer: Outliers : 3.72 % Allowed : 24.57 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.36), residues: 534 helix: 1.37 (0.32), residues: 261 sheet: 0.51 (0.81), residues: 38 loop : -0.75 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 23 TYR 0.008 0.001 TYRBa 118 PHE 0.011 0.001 PHEBa 28 TRP 0.006 0.001 TRPBa 63 HIS 0.014 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4184) covalent geometry : angle 0.50139 ( 5692) hydrogen bonds : bond 0.03706 ( 189) hydrogen bonds : angle 4.78007 ( 581) link_ALPHA1-4 : bond 0.00469 ( 1) link_ALPHA1-4 : angle 1.57956 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: Ba 137 ASP cc_start: 0.9116 (t0) cc_final: 0.8842 (t0) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.0581 time to fit residues: 5.3398 Evaluate side-chains 68 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121585 restraints weight = 8152.912| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.71 r_work: 0.3343 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4185 Z= 0.171 Angle : 0.532 5.371 5695 Z= 0.272 Chirality : 0.041 0.135 633 Planarity : 0.004 0.047 737 Dihedral : 4.286 47.822 607 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 4.71 % Allowed : 24.32 % Favored : 70.97 % 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 are not related in a simple way. whole: 0.39 (0.35), residues: 534 helix: 1.23 (0.31), residues: 262 sheet: 0.43 (0.99), residues: 24 loop : -0.81 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 317 TYR 0.009 0.001 TYRBa 118 PHE 0.014 0.001 PHEBa 28 TRP 0.007 0.001 TRPBa 63 HIS 0.011 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4184) covalent geometry : angle 0.53130 ( 5692) hydrogen bonds : bond 0.03902 ( 189) hydrogen bonds : angle 4.77085 ( 581) link_ALPHA1-4 : bond 0.00569 ( 1) link_ALPHA1-4 : angle 1.61881 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.156 Fit side-chains REVERT: Ba 137 ASP cc_start: 0.9126 (t0) cc_final: 0.8836 (t0) REVERT: Ba 176 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6773 (pttt) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.0678 time to fit residues: 6.5240 Evaluate side-chains 73 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain Ba residue 364 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.146667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121477 restraints weight = 13073.762| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.85 r_work: 0.3283 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4185 Z= 0.164 Angle : 0.533 5.374 5695 Z= 0.272 Chirality : 0.041 0.128 633 Planarity : 0.004 0.049 737 Dihedral : 4.416 47.942 607 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 3.97 % Allowed : 25.31 % Favored : 70.72 % 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 are not related in a simple way. whole: 0.34 (0.35), residues: 534 helix: 1.24 (0.31), residues: 262 sheet: 0.38 (0.99), residues: 24 loop : -0.88 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.009 0.001 TYRBa 118 PHE 0.013 0.001 PHEBa 28 TRP 0.006 0.001 TRPBa 63 HIS 0.009 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4184) covalent geometry : angle 0.53151 ( 5692) hydrogen bonds : bond 0.03759 ( 189) hydrogen bonds : angle 4.69987 ( 581) link_ALPHA1-4 : bond 0.00591 ( 1) link_ALPHA1-4 : angle 1.75964 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: Ba 137 ASP cc_start: 0.9173 (t0) cc_final: 0.8860 (t0) REVERT: Ba 176 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6820 (pttt) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.0712 time to fit residues: 6.8720 Evaluate side-chains 75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain Ba residue 364 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120646 restraints weight = 14217.521| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.96 r_work: 0.3276 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4185 Z= 0.159 Angle : 0.537 5.383 5695 Z= 0.273 Chirality : 0.041 0.129 633 Planarity : 0.004 0.049 737 Dihedral : 4.381 48.176 607 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 4.71 % Allowed : 24.81 % Favored : 70.47 % 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 are not related in a simple way. whole: 0.34 (0.35), residues: 534 helix: 1.28 (0.31), residues: 262 sheet: 0.16 (0.78), residues: 41 loop : -0.98 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.009 0.001 TYRBa 118 PHE 0.012 0.001 PHEBa 28 TRP 0.007 0.001 TRPBa 63 HIS 0.008 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4184) covalent geometry : angle 0.53544 ( 5692) hydrogen bonds : bond 0.03667 ( 189) hydrogen bonds : angle 4.69432 ( 581) link_ALPHA1-4 : bond 0.00522 ( 1) link_ALPHA1-4 : angle 1.61076 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: Ba 50 GLN cc_start: 0.9164 (mt0) cc_final: 0.8954 (mp10) REVERT: Ba 137 ASP cc_start: 0.9145 (t0) cc_final: 0.8881 (t0) REVERT: Ba 176 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6854 (pttt) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.0745 time to fit residues: 7.2496 Evaluate side-chains 79 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 300 LEU Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain Ba residue 364 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.147967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122772 restraints weight = 8617.858| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.80 r_work: 0.3361 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4185 Z= 0.128 Angle : 0.515 5.426 5695 Z= 0.263 Chirality : 0.040 0.127 633 Planarity : 0.004 0.050 737 Dihedral : 4.277 47.979 607 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 3.47 % Allowed : 26.05 % Favored : 70.47 % 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 are not related in a simple way. whole: 0.46 (0.35), residues: 534 helix: 1.37 (0.31), residues: 263 sheet: 0.52 (0.81), residues: 38 loop : -0.97 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.008 0.001 TYRBa 118 PHE 0.010 0.001 PHEBa 28 TRP 0.007 0.001 TRPBa 159 HIS 0.007 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4184) covalent geometry : angle 0.51439 ( 5692) hydrogen bonds : bond 0.03317 ( 189) hydrogen bonds : angle 4.57479 ( 581) link_ALPHA1-4 : bond 0.00331 ( 1) link_ALPHA1-4 : angle 1.47975 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: Ba 137 ASP cc_start: 0.9079 (t0) cc_final: 0.8723 (t0) REVERT: Ba 176 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6748 (pttt) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.0786 time to fit residues: 7.6353 Evaluate side-chains 76 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 300 LEU Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.147658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121914 restraints weight = 14407.126| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.91 r_work: 0.3295 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4185 Z= 0.133 Angle : 0.514 5.297 5695 Z= 0.262 Chirality : 0.040 0.127 633 Planarity : 0.004 0.050 737 Dihedral : 4.250 47.992 607 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 3.47 % Allowed : 25.81 % Favored : 70.72 % 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 are not related in a simple way. whole: 0.45 (0.35), residues: 534 helix: 1.47 (0.31), residues: 257 sheet: 0.55 (0.80), residues: 38 loop : -1.06 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.009 0.001 TYRBa 118 PHE 0.010 0.001 PHEBa 28 TRP 0.007 0.001 TRPBa 63 HIS 0.007 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4184) covalent geometry : angle 0.51308 ( 5692) hydrogen bonds : bond 0.03340 ( 189) hydrogen bonds : angle 4.56846 ( 581) link_ALPHA1-4 : bond 0.00395 ( 1) link_ALPHA1-4 : angle 1.47688 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: Ba 46 GLU cc_start: 0.8192 (mp0) cc_final: 0.7597 (mp0) REVERT: Ba 50 GLN cc_start: 0.9112 (mt0) cc_final: 0.8834 (mp10) REVERT: Ba 137 ASP cc_start: 0.9103 (t0) cc_final: 0.8733 (t0) REVERT: Ba 176 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6784 (pttt) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.0755 time to fit residues: 7.0719 Evaluate side-chains 75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 300 LEU Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 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 = 0.3783 r_free = 0.3783 target = 0.142879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118690 restraints weight = 13918.602| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.69 r_work: 0.3310 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4185 Z= 0.138 Angle : 0.523 5.292 5695 Z= 0.266 Chirality : 0.040 0.136 633 Planarity : 0.004 0.050 737 Dihedral : 4.260 48.101 607 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 3.47 % Allowed : 26.05 % Favored : 70.47 % 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 are not related in a simple way. whole: 0.42 (0.35), residues: 534 helix: 1.44 (0.31), residues: 257 sheet: 0.56 (0.80), residues: 38 loop : -1.07 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.009 0.001 TYRBa 118 PHE 0.011 0.001 PHEBa 28 TRP 0.007 0.001 TRPBa 63 HIS 0.007 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4184) covalent geometry : angle 0.52167 ( 5692) hydrogen bonds : bond 0.03366 ( 189) hydrogen bonds : angle 4.53711 ( 581) link_ALPHA1-4 : bond 0.00363 ( 1) link_ALPHA1-4 : angle 1.48605 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: Ba 46 GLU cc_start: 0.8109 (mp0) cc_final: 0.7526 (mp0) REVERT: Ba 50 GLN cc_start: 0.9082 (mt0) cc_final: 0.8799 (mp10) REVERT: Ba 137 ASP cc_start: 0.9075 (t0) cc_final: 0.8723 (t0) REVERT: Ba 176 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6801 (pttt) outliers start: 14 outliers final: 12 residues processed: 73 average time/residue: 0.0715 time to fit residues: 6.6317 Evaluate side-chains 75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 300 LEU Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.140500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117250 restraints weight = 12816.656| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.18 r_work: 0.3298 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4185 Z= 0.203 Angle : 0.576 5.476 5695 Z= 0.293 Chirality : 0.042 0.139 633 Planarity : 0.004 0.048 737 Dihedral : 4.488 48.903 607 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.66 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 26.05 % Favored : 70.47 % 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 are not related in a simple way. whole: 0.17 (0.35), residues: 534 helix: 1.24 (0.31), residues: 256 sheet: 0.49 (0.97), residues: 24 loop : -1.12 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.009 0.001 TYRBa 118 PHE 0.015 0.002 PHEBa 28 TRP 0.010 0.001 TRPBa 63 HIS 0.008 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 4184) covalent geometry : angle 0.57515 ( 5692) hydrogen bonds : bond 0.03967 ( 189) hydrogen bonds : angle 4.69038 ( 581) link_ALPHA1-4 : bond 0.00691 ( 1) link_ALPHA1-4 : angle 1.69699 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: Ba 83 ASP cc_start: 0.8338 (t0) cc_final: 0.8111 (p0) REVERT: Ba 137 ASP cc_start: 0.9114 (t0) cc_final: 0.8742 (t0) REVERT: Ba 176 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6869 (pttt) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.0624 time to fit residues: 5.4822 Evaluate side-chains 72 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 3 ILE Chi-restraints excluded: chain Ba residue 54 THR Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 182 VAL Chi-restraints excluded: chain Ba residue 259 PHE Chi-restraints excluded: chain Ba residue 346 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 17 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121294 restraints weight = 14017.128| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.75 r_work: 0.3333 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4185 Z= 0.102 Angle : 0.511 6.003 5695 Z= 0.262 Chirality : 0.039 0.135 633 Planarity : 0.004 0.052 737 Dihedral : 4.224 48.184 607 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 28.04 % Favored : 70.22 % 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 are not related in a simple way. whole: 0.53 (0.36), residues: 534 helix: 1.54 (0.32), residues: 257 sheet: 0.59 (0.80), residues: 38 loop : -1.03 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBa 99 TYR 0.007 0.001 TYRBa 118 PHE 0.006 0.001 PHEBa 28 TRP 0.009 0.001 TRPBa 159 HIS 0.005 0.001 HISBa 372 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 4184) covalent geometry : angle 0.51013 ( 5692) hydrogen bonds : bond 0.02931 ( 189) hydrogen bonds : angle 4.46492 ( 581) link_ALPHA1-4 : bond 0.00087 ( 1) link_ALPHA1-4 : angle 1.31925 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.67 seconds wall clock time: 21 minutes 53.52 seconds (1313.52 seconds total)