Starting phenix.real_space_refine on Thu Jul 2 09:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp8_25368/07_2026/7sp8_25368.map" } resolution = 2.7 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= -0.001 sd= 0.791 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1820 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3935 2.51 5 N 999 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4176 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MN': 2, '3PE': 1, 'UD1': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 303 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 303 " occ=0.50 Time building chain proxies: 2.09, per 1000 atoms: 0.34 Number of scatterers: 6090 At special positions: 0 Unit cell: (73.44, 72.36, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1116 8.00 N 999 7.00 C 3935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.51 Conformation dependent library (CDL) restraints added in 439.3 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 47.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.648A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.655A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.509A pdb=" N SER A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.560A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.051A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 5.221A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 357 removed outlier: 4.281A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.507A pdb=" N GLN A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.707A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 4.031A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 468 through 497 removed outlier: 4.083A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.750A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.522A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.656A pdb=" N ILE A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.554A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.630A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.292A pdb=" N VAL B 12 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.592A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.050A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 93 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY C 119 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 95 " --> pdb=" O GLY C 117 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 942 1.31 - 1.43: 1856 1.43 - 1.56: 3363 1.56 - 1.69: 28 1.69 - 1.81: 53 Bond restraints: 6242 Sorted by residual: bond pdb=" C2B UD1 A 601 " pdb=" C3B UD1 A 601 " ideal model delta sigma weight residual 1.533 1.303 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C5 UD1 A 601 " pdb=" C6 UD1 A 601 " ideal model delta sigma weight residual 1.342 1.484 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 UD1 A 601 " pdb=" N3 UD1 A 601 " ideal model delta sigma weight residual 1.371 1.501 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" CBD Y01 A 603 " pdb=" CBG Y01 A 603 " ideal model delta sigma weight residual 1.520 1.644 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C7' UD1 A 601 " pdb=" N2' UD1 A 601 " ideal model delta sigma weight residual 1.347 1.465 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 6237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 8374 3.27 - 6.55: 74 6.55 - 9.82: 13 9.82 - 13.10: 4 13.10 - 16.37: 4 Bond angle restraints: 8469 Sorted by residual: angle pdb=" O1' UD1 A 601 " pdb=" PB UD1 A 601 " pdb=" O3A UD1 A 601 " ideal model delta sigma weight residual 92.88 109.25 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O3A UD1 A 601 " pdb=" PA UD1 A 601 " pdb=" O5B UD1 A 601 " ideal model delta sigma weight residual 94.40 109.61 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O12 3PE A 602 " pdb=" P 3PE A 602 " pdb=" O14 3PE A 602 " ideal model delta sigma weight residual 123.79 109.19 14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAM Y01 A 603 " pdb=" CAY Y01 A 603 " pdb=" OAW Y01 A 603 " ideal model delta sigma weight residual 111.19 124.36 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " pdb=" CAV Y01 A 603 " ideal model delta sigma weight residual 120.03 131.68 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 8464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3227 17.18 - 34.36: 294 34.36 - 51.54: 58 51.54 - 68.72: 16 68.72 - 85.90: 7 Dihedral angle restraints: 3602 sinusoidal: 1436 harmonic: 2166 Sorted by residual: dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ARG A 549 " pdb=" CA ARG A 549 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP C 59 " pdb=" CB ASP C 59 " pdb=" CG ASP C 59 " pdb=" OD1 ASP C 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.64 54.64 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CB MET A 438 " pdb=" CG MET A 438 " pdb=" SD MET A 438 " pdb=" CE MET A 438 " ideal model delta sinusoidal sigma weight residual 60.00 119.74 -59.74 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 844 0.079 - 0.158: 62 0.158 - 0.237: 8 0.237 - 0.316: 2 0.316 - 0.395: 3 Chirality restraints: 919 Sorted by residual: chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CBE Y01 A 603 " pdb=" CAP Y01 A 603 " pdb=" CBB Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBI Y01 A 603 " pdb=" CAU Y01 A 603 " pdb=" CBE Y01 A 603 " pdb=" CBG Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 916 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 544 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C GLU A 544 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 544 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 545 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 87 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 545 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C LEU A 545 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU A 545 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 546 " -0.007 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 454 2.74 - 3.28: 5804 3.28 - 3.82: 10316 3.82 - 4.36: 11542 4.36 - 4.90: 20548 Nonbonded interactions: 48664 Sorted by model distance: nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 605 " model vdw 2.204 2.320 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 604 " model vdw 2.247 2.320 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN A 506 " pdb=" OG1 THR B 56 " model vdw 2.296 3.040 nonbonded pdb=" OD2 ASP B 104 " pdb=" OG1 THR B 107 " model vdw 2.321 3.040 ... (remaining 48659 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.040 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:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.008 0.230 6244 Z= 0.376 Angle : 0.770 16.370 8473 Z= 0.303 Chirality : 0.049 0.395 919 Planarity : 0.003 0.031 1040 Dihedral : 14.245 85.904 2218 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.37 % 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: 2.53 (0.32), residues: 735 helix: 2.59 (0.30), residues: 316 sheet: 2.50 (0.42), residues: 161 loop : -0.08 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.008 0.001 TYR A 414 PHE 0.014 0.001 PHE A 49 TRP 0.007 0.000 TRP A 346 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.38 ( 6242) covalent geometry : angle 0.77007 / 0.30 ( 8469) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.14079 / 0.07 ( 4) hydrogen bonds : bond 0.19500 / 12.98 ( 324) hydrogen bonds : angle 6.37910 / 4.67 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.293 Fit side-chains REVERT: C 28 ILE cc_start: 0.7720 (mm) cc_final: 0.7186 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.4335 time to fit residues: 64.8408 Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 537 ASN B 39 GLN B 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074637 restraints weight = 32128.800| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.34 r_work: 0.2920 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6244 Z= 0.151 Angle : 0.569 7.073 8473 Z= 0.294 Chirality : 0.043 0.164 919 Planarity : 0.004 0.033 1040 Dihedral : 6.770 51.122 884 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.09 % Favored : 98.77 % Rotamer: Outliers : 4.27 % Allowed : 9.00 % Favored : 86.73 % 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: 2.22 (0.31), residues: 735 helix: 2.54 (0.29), residues: 320 sheet: 1.88 (0.41), residues: 154 loop : -0.16 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.015 0.002 TYR A 414 PHE 0.016 0.002 PHE A 49 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6242) covalent geometry : angle 0.56872 / 0.29 ( 8469) SS BOND : bond 0.00292 / 0.15 ( 2) SS BOND : angle 0.64064 / 0.33 ( 4) hydrogen bonds : bond 0.04579 / 3.03 ( 324) hydrogen bonds : angle 4.36355 / 3.22 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.242 Fit side-chains REVERT: B 3 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7558 (mp-120) REVERT: C 25 SER cc_start: 0.9234 (m) cc_final: 0.8902 (p) outliers start: 26 outliers final: 8 residues processed: 129 average time/residue: 0.4513 time to fit residues: 61.7306 Evaluate side-chains 121 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN A 339 GLN B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072632 restraints weight = 32191.341| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.33 r_work: 0.2880 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6244 Z= 0.115 Angle : 0.511 8.886 8473 Z= 0.267 Chirality : 0.042 0.156 919 Planarity : 0.003 0.031 1040 Dihedral : 6.675 52.711 884 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.48 % Allowed : 12.95 % Favored : 83.57 % 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: 2.21 (0.31), residues: 735 helix: 2.47 (0.29), residues: 320 sheet: 2.15 (0.40), residues: 149 loop : -0.22 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 66 TYR 0.016 0.001 TYR A 414 PHE 0.015 0.001 PHE A 49 TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6242) covalent geometry : angle 0.51088 / 0.27 ( 8469) SS BOND : bond 0.00373 / 0.19 ( 2) SS BOND : angle 0.32977 / 0.17 ( 4) hydrogen bonds : bond 0.04363 / 2.93 ( 324) hydrogen bonds : angle 4.12073 / 3.06 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.243 Fit side-chains REVERT: C 11 LEU cc_start: 0.8048 (tm) cc_final: 0.7788 (tt) outliers start: 21 outliers final: 10 residues processed: 120 average time/residue: 0.4706 time to fit residues: 59.7930 Evaluate side-chains 111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 506 GLN B 73 ASN C 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070647 restraints weight = 28040.996| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.08 r_work: 0.2846 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6244 Z= 0.122 Angle : 0.511 7.904 8473 Z= 0.268 Chirality : 0.041 0.142 919 Planarity : 0.003 0.036 1040 Dihedral : 6.725 53.311 884 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.79 % Allowed : 13.59 % Favored : 82.62 % 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: 2.04 (0.31), residues: 735 helix: 2.31 (0.29), residues: 322 sheet: 1.89 (0.40), residues: 161 loop : -0.30 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.016 0.001 TYR A 414 PHE 0.016 0.001 PHE A 49 TRP 0.018 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6242) covalent geometry : angle 0.51143 / 0.27 ( 8469) SS BOND : bond 0.00333 / 0.17 ( 2) SS BOND : angle 0.38998 / 0.20 ( 4) hydrogen bonds : bond 0.04402 / 2.93 ( 324) hydrogen bonds : angle 4.06204 / 3.03 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.234 Fit side-chains REVERT: B 18 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8539 (mm) outliers start: 22 outliers final: 10 residues processed: 112 average time/residue: 0.5097 time to fit residues: 60.1307 Evaluate side-chains 110 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072235 restraints weight = 20126.740| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.60 r_work: 0.2891 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6244 Z= 0.106 Angle : 0.497 6.771 8473 Z= 0.259 Chirality : 0.042 0.232 919 Planarity : 0.003 0.037 1040 Dihedral : 6.656 56.537 884 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.79 % Allowed : 14.69 % Favored : 81.52 % 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: 2.07 (0.30), residues: 735 helix: 2.41 (0.29), residues: 320 sheet: 2.02 (0.39), residues: 149 loop : -0.33 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.017 0.001 TYR C 106 PHE 0.014 0.001 PHE A 49 TRP 0.021 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 6242) covalent geometry : angle 0.49730 / 0.26 ( 8469) SS BOND : bond 0.00363 / 0.18 ( 2) SS BOND : angle 0.24251 / 0.13 ( 4) hydrogen bonds : bond 0.04126 / 2.76 ( 324) hydrogen bonds : angle 4.00156 / 2.98 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.260 Fit side-chains REVERT: A 544 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: B 18 LEU cc_start: 0.8765 (mt) cc_final: 0.8532 (mm) REVERT: C 11 LEU cc_start: 0.8260 (tm) cc_final: 0.8016 (tt) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 0.4791 time to fit residues: 57.6597 Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.0370 chunk 12 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 331 ASN B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072391 restraints weight = 34028.670| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.40 r_work: 0.2875 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6244 Z= 0.099 Angle : 0.507 8.171 8473 Z= 0.259 Chirality : 0.041 0.173 919 Planarity : 0.003 0.037 1040 Dihedral : 6.513 57.617 884 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.53 % Allowed : 17.06 % Favored : 80.41 % 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: 2.08 (0.30), residues: 735 helix: 2.45 (0.29), residues: 319 sheet: 1.90 (0.39), residues: 150 loop : -0.30 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.019 0.001 TYR C 106 PHE 0.014 0.001 PHE A 49 TRP 0.028 0.001 TRP A 472 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6242) covalent geometry : angle 0.50721 / 0.26 ( 8469) SS BOND : bond 0.00351 / 0.18 ( 2) SS BOND : angle 0.24701 / 0.14 ( 4) hydrogen bonds : bond 0.03854 / 2.58 ( 324) hydrogen bonds : angle 3.93735 / 2.95 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.245 Fit side-chains REVERT: B 18 LEU cc_start: 0.8754 (mt) cc_final: 0.8521 (mm) REVERT: C 11 LEU cc_start: 0.8126 (tm) cc_final: 0.7862 (tt) outliers start: 14 outliers final: 9 residues processed: 110 average time/residue: 0.4734 time to fit residues: 55.0108 Evaluate side-chains 108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 331 ASN A 338 GLN A 339 GLN B 73 ASN B 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.070069 restraints weight = 24397.722| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.87 r_work: 0.2839 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6244 Z= 0.129 Angle : 0.538 7.298 8473 Z= 0.281 Chirality : 0.042 0.178 919 Planarity : 0.003 0.039 1040 Dihedral : 6.653 58.586 884 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.53 % Allowed : 17.85 % Favored : 79.62 % 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: 2.04 (0.31), residues: 735 helix: 2.39 (0.29), residues: 321 sheet: 1.82 (0.39), residues: 161 loop : -0.36 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.020 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.028 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6242) covalent geometry : angle 0.53809 / 0.28 ( 8469) SS BOND : bond 0.00361 / 0.18 ( 2) SS BOND : angle 0.20968 / 0.11 ( 4) hydrogen bonds : bond 0.04418 / 2.95 ( 324) hydrogen bonds : angle 3.99556 / 2.98 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.252 Fit side-chains REVERT: A 247 ARG cc_start: 0.8835 (tpp-160) cc_final: 0.8578 (tpm-80) REVERT: B 18 LEU cc_start: 0.8815 (mt) cc_final: 0.8566 (mm) REVERT: B 72 ASP cc_start: 0.8444 (t0) cc_final: 0.8163 (t0) REVERT: C 11 LEU cc_start: 0.8213 (tm) cc_final: 0.7941 (tt) REVERT: C 25 SER cc_start: 0.9168 (m) cc_final: 0.8821 (p) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.4840 time to fit residues: 57.3607 Evaluate side-chains 114 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070143 restraints weight = 22741.244| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.75 r_work: 0.2844 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6244 Z= 0.124 Angle : 0.542 8.104 8473 Z= 0.280 Chirality : 0.042 0.163 919 Planarity : 0.003 0.039 1040 Dihedral : 6.676 59.653 884 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.09 % Favored : 98.77 % Rotamer: Outliers : 2.37 % Allowed : 18.64 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.03 (0.30), residues: 735 helix: 2.40 (0.29), residues: 321 sheet: 1.75 (0.39), residues: 161 loop : -0.34 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.020 0.001 TYR C 106 PHE 0.014 0.001 PHE A 49 TRP 0.029 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6242) covalent geometry : angle 0.54191 / 0.28 ( 8469) SS BOND : bond 0.00458 / 0.23 ( 2) SS BOND : angle 0.24852 / 0.14 ( 4) hydrogen bonds : bond 0.04340 / 2.89 ( 324) hydrogen bonds : angle 3.98880 / 2.98 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.233 Fit side-chains REVERT: A 247 ARG cc_start: 0.8799 (tpp-160) cc_final: 0.8572 (tpm-80) REVERT: B 18 LEU cc_start: 0.8862 (mt) cc_final: 0.8606 (mm) REVERT: B 72 ASP cc_start: 0.8288 (t0) cc_final: 0.8014 (t0) REVERT: C 11 LEU cc_start: 0.8230 (tm) cc_final: 0.7951 (tt) REVERT: C 25 SER cc_start: 0.9130 (m) cc_final: 0.8834 (p) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.4716 time to fit residues: 55.9228 Evaluate side-chains 111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 8 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070237 restraints weight = 26050.568| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.96 r_work: 0.2840 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6244 Z= 0.115 Angle : 0.527 6.995 8473 Z= 0.276 Chirality : 0.042 0.176 919 Planarity : 0.003 0.038 1040 Dihedral : 6.601 59.230 884 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.21 % Allowed : 18.64 % Favored : 79.15 % 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: 2.04 (0.30), residues: 735 helix: 2.47 (0.29), residues: 319 sheet: 1.70 (0.39), residues: 162 loop : -0.37 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.020 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.031 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6242) covalent geometry : angle 0.52742 / 0.28 ( 8469) SS BOND : bond 0.00415 / 0.21 ( 2) SS BOND : angle 0.31091 / 0.17 ( 4) hydrogen bonds : bond 0.04191 / 2.79 ( 324) hydrogen bonds : angle 3.95925 / 2.95 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.293 Fit side-chains REVERT: A 348 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8276 (ttm110) REVERT: B 3 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7816 (mp10) REVERT: B 18 LEU cc_start: 0.8831 (mt) cc_final: 0.8579 (mm) REVERT: B 72 ASP cc_start: 0.8309 (t0) cc_final: 0.8008 (t0) REVERT: C 25 SER cc_start: 0.9106 (m) cc_final: 0.8820 (p) REVERT: C 43 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8536 (mtmm) REVERT: C 89 ASP cc_start: 0.8330 (m-30) cc_final: 0.8032 (m-30) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.4847 time to fit residues: 54.9619 Evaluate side-chains 108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 29 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070629 restraints weight = 22241.042| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.73 r_work: 0.2853 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6244 Z= 0.118 Angle : 0.555 8.074 8473 Z= 0.286 Chirality : 0.042 0.170 919 Planarity : 0.003 0.038 1040 Dihedral : 6.572 58.699 884 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.90 % Allowed : 19.43 % Favored : 78.67 % 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: 1.98 (0.30), residues: 735 helix: 2.46 (0.29), residues: 319 sheet: 1.67 (0.39), residues: 162 loop : -0.46 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.019 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.032 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6242) covalent geometry : angle 0.55556 / 0.29 ( 8469) SS BOND : bond 0.00414 / 0.20 ( 2) SS BOND : angle 0.32272 / 0.18 ( 4) hydrogen bonds : bond 0.04195 / 2.79 ( 324) hydrogen bonds : angle 3.94997 / 2.95 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.257 Fit side-chains REVERT: A 348 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8206 (ttm110) REVERT: B 3 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7817 (mp10) REVERT: B 18 LEU cc_start: 0.8824 (mt) cc_final: 0.8585 (mm) REVERT: B 72 ASP cc_start: 0.8296 (t0) cc_final: 0.7938 (t0) REVERT: C 11 LEU cc_start: 0.8394 (tm) cc_final: 0.8153 (tt) REVERT: C 25 SER cc_start: 0.9057 (m) cc_final: 0.8775 (p) outliers start: 10 outliers final: 9 residues processed: 109 average time/residue: 0.5162 time to fit residues: 59.3652 Evaluate side-chains 108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.068982 restraints weight = 32559.918| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.30 r_work: 0.2801 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6244 Z= 0.128 Angle : 0.555 8.006 8473 Z= 0.290 Chirality : 0.042 0.172 919 Planarity : 0.003 0.039 1040 Dihedral : 6.636 58.428 884 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.21 % Allowed : 19.43 % Favored : 78.36 % 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: 1.94 (0.30), residues: 735 helix: 2.40 (0.29), residues: 321 sheet: 1.55 (0.39), residues: 164 loop : -0.41 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.016 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.031 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6242) covalent geometry : angle 0.55557 / 0.29 ( 8469) SS BOND : bond 0.00417 / 0.21 ( 2) SS BOND : angle 0.28222 / 0.16 ( 4) hydrogen bonds : bond 0.04345 / 2.89 ( 324) hydrogen bonds : angle 3.97719 / 2.97 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.63 seconds wall clock time: 41 minutes 59.48 seconds (2519.48 seconds total)