Starting phenix.real_space_refine on Thu Feb 5 03:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3t_62028/02_2026/9k3t_62028.cif" } resolution = 3.15 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= 1.000 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 C 4709 2.51 5 N 1250 2.21 5 O 1434 1.98 5 H 7175 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14609 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5273 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1647 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1812 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "l" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2729 Classifications: {'peptide': 182} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 170} Chain: "h" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3148 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ILE L 83 " occ=0.85 ... (17 atoms not shown) pdb="HD13 ILE L 83 " occ=0.85 Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 14609 At special positions: 0 Unit cell: (67.937, 107.705, 133.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 O 1434 8.00 N 1250 7.00 C 4709 6.00 H 7175 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 465 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 92 " distance=2.03 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 97 " distance=2.03 Simple disulfide: pdb=" SG CYS h 149 " - pdb=" SG CYS h 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 464.4 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 7.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.550A pdb=" N GLY A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.823A pdb=" N GLU A 299 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 477 through 490 removed outlier: 5.016A pdb=" N ASP A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'l' and resid 83 through 87 removed outlier: 3.523A pdb=" N ALA l 87 " --> pdb=" O GLU l 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 130 removed outlier: 3.963A pdb=" N LEU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 125 through 130' Processing helix chain 'l' and resid 153 through 157 Processing helix chain 'h' and resid 29 through 33 Processing helix chain 'h' and resid 88 through 92 Processing helix chain 'h' and resid 165 through 167 No H-bonds generated for 'chain 'h' and resid 165 through 167' Processing helix chain 'h' and resid 195 through 200 removed outlier: 3.936A pdb=" N SER h 199 " --> pdb=" O ASN h 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 152 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 200 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 212 Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 284 removed outlier: 3.645A pdb=" N CYS A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 271 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS A 350 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 331 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 348 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 383 removed outlier: 3.786A pdb=" N LEU A 403 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 473 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 445 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 382 " --> pdb=" O PRO A 444 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 448 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 378 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.538A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.538A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.480A pdb=" N GLU H 11 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN H 40 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE H 35 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.480A pdb=" N GLU H 11 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS H 97 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP H 111 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG H 99 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA H 109 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU H 107 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.638A pdb=" N THR H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'l' and resid 10 through 14 removed outlier: 3.526A pdb=" N TYR l 90 " --> pdb=" O THR l 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'l' and resid 10 through 14 removed outlier: 3.526A pdb=" N TYR l 90 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR l 101 " --> pdb=" O HIS l 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 30 through 31 Processing sheet with id=AB7, first strand: chain 'l' and resid 52 through 53 Processing sheet with id=AB8, first strand: chain 'l' and resid 120 through 122 removed outlier: 3.800A pdb=" N VAL l 137 " --> pdb=" O PHE l 122 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR l 177 " --> pdb=" O ASN l 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'h' and resid 11 through 13 removed outlier: 6.287A pdb=" N GLU h 11 " --> pdb=" O THR h 119 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE h 35 " --> pdb=" O TRP h 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP h 51 " --> pdb=" O ILE h 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP h 37 " --> pdb=" O ILE h 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 11 through 13 removed outlier: 6.287A pdb=" N GLU h 11 " --> pdb=" O THR h 119 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR h 111 " --> pdb=" O ARG h 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.623A pdb=" N SER h 129 " --> pdb=" O LYS h 152 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS h 152 " --> pdb=" O SER h 129 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU h 150 " --> pdb=" O TYR h 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY h 148 " --> pdb=" O LEU h 133 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR h 184 " --> pdb=" O GLY h 153 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER h 187 " --> pdb=" O PRO h 176 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER h 189 " --> pdb=" O THR h 174 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR h 174 " --> pdb=" O SER h 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 160 through 163 241 hydrogen bonds defined for protein. 573 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: 2.89 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7168 1.03 - 1.23: 50 1.23 - 1.42: 3268 1.42 - 1.62: 4261 1.62 - 1.82: 55 Bond restraints: 14802 Sorted by residual: bond pdb=" N ASP A 144 " pdb=" CA ASP A 144 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASP A 144 " pdb=" H ASP A 144 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" CG PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.50e+00 bond pdb=" CB PRO l 81 " pdb=" CG PRO l 81 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.94e-01 bond pdb=" CB PRO l 99 " pdb=" CG PRO l 99 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.81e-01 ... (remaining 14797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 24693 0.91 - 1.82: 1790 1.82 - 2.73: 93 2.73 - 3.64: 43 3.64 - 4.55: 12 Bond angle restraints: 26631 Sorted by residual: angle pdb=" CA TRP h 51 " pdb=" CB TRP h 51 " pdb=" CG TRP h 51 " ideal model delta sigma weight residual 113.60 117.65 -4.05 1.90e+00 2.77e-01 4.54e+00 angle pdb=" N VAL h 120 " pdb=" CA VAL h 120 " pdb=" C VAL h 120 " ideal model delta sigma weight residual 106.53 109.03 -2.50 1.41e+00 5.03e-01 3.14e+00 angle pdb=" C GLU h 157 " pdb=" N PRO h 158 " pdb=" CA PRO h 158 " ideal model delta sigma weight residual 127.00 131.18 -4.18 2.40e+00 1.74e-01 3.04e+00 angle pdb=" N LEU L 94 " pdb=" CA LEU L 94 " pdb=" C LEU L 94 " ideal model delta sigma weight residual 109.32 106.12 3.20 1.84e+00 2.95e-01 3.03e+00 angle pdb=" N ALA l 55 " pdb=" CA ALA l 55 " pdb=" C ALA l 55 " ideal model delta sigma weight residual 110.80 114.40 -3.60 2.13e+00 2.20e-01 2.86e+00 ... (remaining 26626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6289 17.61 - 35.21: 565 35.21 - 52.82: 196 52.82 - 70.43: 47 70.43 - 88.03: 8 Dihedral angle restraints: 7105 sinusoidal: 3773 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " pdb=" SG CYS A 297 " pdb=" CB CYS A 297 " ideal model delta sinusoidal sigma weight residual 93.00 167.96 -74.96 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 92 " pdb=" CB CYS l 92 " ideal model delta sinusoidal sigma weight residual 93.00 59.97 33.03 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS h 23 " pdb=" SG CYS h 23 " pdb=" SG CYS h 97 " pdb=" CB CYS h 97 " ideal model delta sinusoidal sigma weight residual 93.00 61.76 31.24 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 7102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 584 0.028 - 0.055: 373 0.055 - 0.082: 66 0.082 - 0.110: 66 0.110 - 0.137: 37 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CA VAL A 331 " pdb=" N VAL A 331 " pdb=" C VAL A 331 " pdb=" CB VAL A 331 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE l 79 " pdb=" N ILE l 79 " pdb=" C ILE l 79 " pdb=" CB ILE l 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1123 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS l 80 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO l 81 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO l 81 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO l 81 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 287 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 288 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 362 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 363 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.021 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 631 2.17 - 2.77: 28136 2.77 - 3.38: 39066 3.38 - 3.99: 54243 3.99 - 4.60: 83480 Nonbonded interactions: 205556 Sorted by model distance: nonbonded pdb=" HG SER l 95 " pdb=" O GLY h 106 " model vdw 1.558 2.450 nonbonded pdb=" HE2 HIS A 279 " pdb=" O GLY A 439 " model vdw 1.585 2.450 nonbonded pdb="HD21 ASN A 247 " pdb=" O ALA A 266 " model vdw 1.593 2.450 nonbonded pdb="HH12 ARG A 182 " pdb=" OD1 ASN L 93 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR A 416 " pdb=" O PRO A 471 " model vdw 1.636 2.450 ... (remaining 205551 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=0.59 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: 2.400 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.033 7637 Z= 0.133 Angle : 0.484 4.183 10395 Z= 0.255 Chirality : 0.044 0.137 1126 Planarity : 0.004 0.048 1326 Dihedral : 15.495 88.034 2694 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.44 % Allowed : 17.91 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.39 (0.27), residues: 955 helix: -1.65 (0.74), residues: 39 sheet: -0.54 (0.28), residues: 357 loop : -1.11 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG l 18 TYR 0.009 0.001 TYR H 53 PHE 0.006 0.001 PHE h 96 TRP 0.008 0.001 TRP h 51 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7627) covalent geometry : angle 0.48362 (10375) SS BOND : bond 0.00190 ( 10) SS BOND : angle 0.82253 ( 20) hydrogen bonds : bond 0.24998 ( 227) hydrogen bonds : angle 10.67317 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8256 (mmt) cc_final: 0.7414 (mmt) REVERT: A 289 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: A 409 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6300 (mtt180) REVERT: A 488 MET cc_start: 0.7659 (mtp) cc_final: 0.7457 (mtp) REVERT: L 36 TYR cc_start: 0.7777 (m-80) cc_final: 0.7417 (m-80) REVERT: H 75 LYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5003 (mptt) REVERT: l 18 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7345 (ttp-110) REVERT: l 22 SER cc_start: 0.8646 (t) cc_final: 0.8370 (m) REVERT: l 127 GLU cc_start: 0.6257 (mp0) cc_final: 0.5276 (mp0) REVERT: h 2 GLN cc_start: 0.5832 (OUTLIER) cc_final: 0.5436 (pp30) REVERT: h 214 LYS cc_start: 0.4447 (mmtm) cc_final: 0.3782 (mmmt) outliers start: 28 outliers final: 24 residues processed: 115 average time/residue: 0.1786 time to fit residues: 28.1253 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 SER Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 352 GLN H 6 GLN l 128 GLN h 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.197016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.183747 restraints weight = 17458.780| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 0.45 r_work: 0.3721 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7637 Z= 0.216 Angle : 0.580 4.725 10395 Z= 0.315 Chirality : 0.047 0.175 1126 Planarity : 0.005 0.051 1326 Dihedral : 7.070 51.467 1080 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.07 % Allowed : 18.53 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.45 (0.27), residues: 955 helix: -1.56 (0.79), residues: 35 sheet: -0.45 (0.28), residues: 353 loop : -1.26 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 182 TYR 0.014 0.002 TYR H 53 PHE 0.014 0.002 PHE h 30 TRP 0.010 0.002 TRP A 384 HIS 0.012 0.002 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 7627) covalent geometry : angle 0.57822 (10375) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.17243 ( 20) hydrogen bonds : bond 0.05385 ( 227) hydrogen bonds : angle 8.09128 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8607 (mmt) cc_final: 0.7821 (mmt) REVERT: A 260 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: A 409 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6689 (mtt180) REVERT: H 75 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.5704 (mptt) REVERT: l 22 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (m) REVERT: l 127 GLU cc_start: 0.7056 (mp0) cc_final: 0.6159 (mp0) REVERT: l 128 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6124 (tt0) REVERT: h 214 LYS cc_start: 0.5034 (mmtm) cc_final: 0.4498 (mmmt) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.1840 time to fit residues: 29.0610 Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** l 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.199604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.186698 restraints weight = 17344.303| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 0.47 r_work: 0.3756 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7637 Z= 0.140 Angle : 0.521 4.537 10395 Z= 0.280 Chirality : 0.045 0.155 1126 Planarity : 0.004 0.050 1326 Dihedral : 5.588 46.601 1056 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.94 % Allowed : 18.65 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.32 (0.27), residues: 955 helix: -1.37 (0.82), residues: 36 sheet: -0.36 (0.28), residues: 352 loop : -1.18 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG l 18 TYR 0.011 0.001 TYR H 53 PHE 0.011 0.001 PHE h 30 TRP 0.008 0.001 TRP H 37 HIS 0.009 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7627) covalent geometry : angle 0.51919 (10375) SS BOND : bond 0.00343 ( 10) SS BOND : angle 1.02175 ( 20) hydrogen bonds : bond 0.04016 ( 227) hydrogen bonds : angle 7.37282 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8662 (mmt) cc_final: 0.7993 (mmt) REVERT: A 260 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 409 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6794 (mtt180) REVERT: H 75 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.5924 (mptt) REVERT: l 22 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8453 (m) REVERT: l 127 GLU cc_start: 0.7007 (mp0) cc_final: 0.6174 (mp0) REVERT: h 2 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6167 (pp30) REVERT: h 214 LYS cc_start: 0.5132 (mmtm) cc_final: 0.4608 (mmmt) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.1897 time to fit residues: 28.5967 Evaluate side-chains 109 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 180 SER Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 188 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN l 128 GLN h 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.196509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.183552 restraints weight = 17317.856| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.47 r_work: 0.3780 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7637 Z= 0.235 Angle : 0.584 4.950 10395 Z= 0.312 Chirality : 0.047 0.149 1126 Planarity : 0.005 0.054 1326 Dihedral : 5.368 46.385 1049 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.03 % Allowed : 17.30 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.48 (0.27), residues: 955 helix: -1.77 (0.75), residues: 35 sheet: -0.38 (0.28), residues: 349 loop : -1.33 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG l 18 TYR 0.016 0.002 TYR H 53 PHE 0.011 0.002 PHE h 30 TRP 0.011 0.002 TRP H 37 HIS 0.010 0.002 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 7627) covalent geometry : angle 0.58117 (10375) SS BOND : bond 0.00445 ( 10) SS BOND : angle 1.50118 ( 20) hydrogen bonds : bond 0.03956 ( 227) hydrogen bonds : angle 7.15109 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8509 (mmt) cc_final: 0.7846 (mmt) REVERT: A 260 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: A 409 ARG cc_start: 0.7224 (ttm170) cc_final: 0.6801 (mtt180) REVERT: A 420 ILE cc_start: 0.7760 (pt) cc_final: 0.7349 (pt) REVERT: H 75 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6016 (mptt) REVERT: l 22 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8378 (m) REVERT: l 127 GLU cc_start: 0.7244 (mp0) cc_final: 0.6496 (mp0) REVERT: h 2 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6321 (pp30) REVERT: h 214 LYS cc_start: 0.5196 (mmtm) cc_final: 0.4810 (mmmt) outliers start: 41 outliers final: 32 residues processed: 126 average time/residue: 0.1812 time to fit residues: 31.7880 Evaluate side-chains 131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 141 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 180 SER Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 188 SER Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.198787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.185048 restraints weight = 17339.804| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 0.47 r_work: 0.3750 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7637 Z= 0.134 Angle : 0.510 4.830 10395 Z= 0.271 Chirality : 0.044 0.144 1126 Planarity : 0.004 0.052 1326 Dihedral : 5.121 47.185 1049 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.58 % Allowed : 18.77 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.33 (0.27), residues: 955 helix: -1.41 (0.81), residues: 36 sheet: -0.38 (0.27), residues: 360 loop : -1.18 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 18 TYR 0.011 0.001 TYR H 53 PHE 0.009 0.001 PHE h 30 TRP 0.009 0.001 TRP h 51 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7627) covalent geometry : angle 0.50849 (10375) SS BOND : bond 0.00325 ( 10) SS BOND : angle 1.08923 ( 20) hydrogen bonds : bond 0.03194 ( 227) hydrogen bonds : angle 6.66049 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.310 Fit side-chains REVERT: A 210 MET cc_start: 0.8472 (mmt) cc_final: 0.7686 (mmt) REVERT: A 260 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 409 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6689 (mtt180) REVERT: A 420 ILE cc_start: 0.7529 (pt) cc_final: 0.7094 (pt) REVERT: H 75 LYS cc_start: 0.6587 (OUTLIER) cc_final: 0.5590 (mptt) REVERT: l 22 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8235 (m) REVERT: l 127 GLU cc_start: 0.6941 (mp0) cc_final: 0.6067 (mp0) REVERT: h 2 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6021 (pp30) REVERT: h 214 LYS cc_start: 0.5072 (mmtm) cc_final: 0.4535 (mmmt) outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.1856 time to fit residues: 27.5934 Evaluate side-chains 109 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 141 ASN Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.200292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.187054 restraints weight = 17239.525| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 0.46 r_work: 0.3760 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7637 Z= 0.118 Angle : 0.491 4.537 10395 Z= 0.259 Chirality : 0.044 0.140 1126 Planarity : 0.004 0.051 1326 Dihedral : 4.932 47.628 1049 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.82 % Allowed : 18.40 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.23 (0.27), residues: 955 helix: -1.26 (0.83), residues: 36 sheet: -0.33 (0.28), residues: 354 loop : -1.10 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.010 0.001 TYR H 53 PHE 0.009 0.001 PHE h 30 TRP 0.008 0.001 TRP A 483 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7627) covalent geometry : angle 0.48939 (10375) SS BOND : bond 0.00341 ( 10) SS BOND : angle 1.02997 ( 20) hydrogen bonds : bond 0.02941 ( 227) hydrogen bonds : angle 6.31714 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8360 (mmt) cc_final: 0.7585 (mmt) REVERT: A 260 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: A 409 ARG cc_start: 0.7056 (ttm170) cc_final: 0.6591 (mtt180) REVERT: H 75 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.5938 (mptt) REVERT: l 73 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7590 (m) REVERT: l 127 GLU cc_start: 0.7241 (mp0) cc_final: 0.6488 (mp0) REVERT: h 2 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6225 (pp30) REVERT: h 214 LYS cc_start: 0.5175 (mmtm) cc_final: 0.4831 (mmmt) outliers start: 23 outliers final: 15 residues processed: 111 average time/residue: 0.1640 time to fit residues: 25.7421 Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.200529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.187003 restraints weight = 17159.362| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 0.48 r_work: 0.3751 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7637 Z= 0.120 Angle : 0.489 4.581 10395 Z= 0.258 Chirality : 0.044 0.139 1126 Planarity : 0.004 0.060 1326 Dihedral : 4.779 47.708 1046 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.07 % Allowed : 17.91 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.21 (0.27), residues: 955 helix: -1.20 (0.84), residues: 36 sheet: -0.36 (0.27), residues: 360 loop : -1.07 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG l 18 TYR 0.010 0.001 TYR H 53 PHE 0.009 0.001 PHE h 30 TRP 0.008 0.001 TRP h 51 HIS 0.008 0.001 HIS l 80 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7627) covalent geometry : angle 0.48728 (10375) SS BOND : bond 0.00342 ( 10) SS BOND : angle 1.02685 ( 20) hydrogen bonds : bond 0.02867 ( 227) hydrogen bonds : angle 6.18541 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8533 (mmt) cc_final: 0.7759 (mmt) REVERT: A 260 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: A 409 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6692 (mtt180) REVERT: H 105 ASP cc_start: 0.8524 (t0) cc_final: 0.8319 (t0) REVERT: l 127 GLU cc_start: 0.7183 (mp0) cc_final: 0.6359 (mp0) REVERT: h 2 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6258 (pp30) REVERT: h 214 LYS cc_start: 0.5180 (mmtm) cc_final: 0.4759 (mmmt) outliers start: 25 outliers final: 22 residues processed: 110 average time/residue: 0.1786 time to fit residues: 27.8093 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 141 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.199321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.186747 restraints weight = 17303.923| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 0.44 r_work: 0.3766 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7637 Z= 0.145 Angle : 0.504 4.688 10395 Z= 0.266 Chirality : 0.044 0.151 1126 Planarity : 0.004 0.052 1326 Dihedral : 4.743 47.575 1042 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.31 % Allowed : 17.67 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.24 (0.27), residues: 955 helix: -1.29 (0.82), residues: 36 sheet: -0.35 (0.27), residues: 360 loop : -1.09 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG l 18 TYR 0.011 0.001 TYR H 53 PHE 0.009 0.001 PHE h 30 TRP 0.008 0.001 TRP A 483 HIS 0.007 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7627) covalent geometry : angle 0.50220 (10375) SS BOND : bond 0.00362 ( 10) SS BOND : angle 1.11621 ( 20) hydrogen bonds : bond 0.02959 ( 227) hydrogen bonds : angle 6.18341 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8577 (mmt) cc_final: 0.7779 (mmt) REVERT: A 260 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: A 289 GLU cc_start: 0.7744 (mp0) cc_final: 0.7521 (mp0) REVERT: A 409 ARG cc_start: 0.7176 (ttm170) cc_final: 0.6707 (mtt180) REVERT: A 420 ILE cc_start: 0.7663 (pt) cc_final: 0.7203 (pt) REVERT: l 73 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7736 (m) REVERT: l 127 GLU cc_start: 0.7121 (mp0) cc_final: 0.6258 (mp0) REVERT: h 2 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6187 (pp30) REVERT: h 214 LYS cc_start: 0.5169 (mmtm) cc_final: 0.4697 (mmmt) outliers start: 27 outliers final: 23 residues processed: 116 average time/residue: 0.1732 time to fit residues: 28.3692 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 141 ASN Chi-restraints excluded: chain l residue 176 THR Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.202224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.188392 restraints weight = 17186.850| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 0.51 r_work: 0.3755 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7637 Z= 0.098 Angle : 0.469 4.498 10395 Z= 0.247 Chirality : 0.044 0.147 1126 Planarity : 0.004 0.051 1326 Dihedral : 4.545 48.133 1042 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.33 % Allowed : 18.65 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.10 (0.27), residues: 955 helix: -1.07 (0.85), residues: 36 sheet: -0.30 (0.27), residues: 360 loop : -0.98 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.007 0.001 TYR L 50 PHE 0.008 0.001 PHE h 30 TRP 0.008 0.001 TRP h 51 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7627) covalent geometry : angle 0.46738 (10375) SS BOND : bond 0.00315 ( 10) SS BOND : angle 0.89254 ( 20) hydrogen bonds : bond 0.02639 ( 227) hydrogen bonds : angle 5.89478 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: A 289 GLU cc_start: 0.7671 (mp0) cc_final: 0.7452 (mp0) REVERT: A 409 ARG cc_start: 0.7069 (ttm170) cc_final: 0.6629 (mtt180) REVERT: l 127 GLU cc_start: 0.7055 (mp0) cc_final: 0.6206 (mp0) REVERT: h 2 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6174 (pp30) REVERT: h 101 ASP cc_start: 0.8405 (p0) cc_final: 0.7875 (p0) REVERT: h 214 LYS cc_start: 0.5151 (mmtm) cc_final: 0.4713 (mmmt) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.1855 time to fit residues: 26.6542 Evaluate side-chains 107 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.199818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.186948 restraints weight = 17364.021| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 0.45 r_work: 0.3766 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7637 Z= 0.166 Angle : 0.515 4.781 10395 Z= 0.272 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.053 1326 Dihedral : 4.730 47.705 1042 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.70 % Allowed : 18.65 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.20 (0.27), residues: 955 helix: -1.28 (0.83), residues: 36 sheet: -0.37 (0.27), residues: 363 loop : -1.03 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.012 0.002 TYR H 53 PHE 0.009 0.001 PHE h 96 TRP 0.008 0.001 TRP A 483 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7627) covalent geometry : angle 0.51295 (10375) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.19556 ( 20) hydrogen bonds : bond 0.03003 ( 227) hydrogen bonds : angle 6.06969 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: A 289 GLU cc_start: 0.7612 (mp0) cc_final: 0.7361 (mp0) REVERT: A 409 ARG cc_start: 0.7193 (ttm170) cc_final: 0.6721 (mtt180) REVERT: A 420 ILE cc_start: 0.7680 (pt) cc_final: 0.7210 (pt) REVERT: l 73 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7743 (m) REVERT: l 127 GLU cc_start: 0.7101 (mp0) cc_final: 0.6292 (mp0) REVERT: h 2 GLN cc_start: 0.6705 (OUTLIER) cc_final: 0.6291 (pp30) REVERT: h 214 LYS cc_start: 0.5197 (mmtm) cc_final: 0.4781 (mmmt) outliers start: 22 outliers final: 18 residues processed: 105 average time/residue: 0.1700 time to fit residues: 24.6344 Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 73 THR Chi-restraints excluded: chain l residue 94 HIS Chi-restraints excluded: chain l residue 138 CYS Chi-restraints excluded: chain l residue 182 THR Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.201144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.187325 restraints weight = 17073.918| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 0.50 r_work: 0.3739 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7637 Z= 0.131 Angle : 0.492 4.610 10395 Z= 0.260 Chirality : 0.044 0.136 1126 Planarity : 0.004 0.052 1326 Dihedral : 4.669 47.682 1042 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.58 % Allowed : 18.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.15 (0.27), residues: 955 helix: -1.21 (0.84), residues: 36 sheet: -0.32 (0.27), residues: 361 loop : -1.01 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.010 0.001 TYR H 53 PHE 0.009 0.001 PHE h 30 TRP 0.008 0.001 TRP h 51 HIS 0.007 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7627) covalent geometry : angle 0.49039 (10375) SS BOND : bond 0.00354 ( 10) SS BOND : angle 1.05090 ( 20) hydrogen bonds : bond 0.02832 ( 227) hydrogen bonds : angle 5.97272 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3536.24 seconds wall clock time: 60 minutes 50.99 seconds (3650.99 seconds total)