Starting phenix.real_space_refine on Thu Jul 2 14:08:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.map" model { file = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y95_39070/07_2026/8y95_39070.cif" } resolution = 3.24 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6042 2.51 5 N 1406 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 9018 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4495 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain: "D" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4495 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Ad-hoc single atom residues: {' CL': 1, ' NA': 1} Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Ad-hoc single atom residues: {' CL': 1, ' NA': 1} Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 9018 At special positions: 0 Unit cell: (100.01, 107.31, 93.44, 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) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1526 8.00 N 1406 7.00 C 6042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 335.2 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 4.005A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.713A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 107 Proline residue: A 97 - end of helix removed outlier: 3.530A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.581A pdb=" N TYR A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.763A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.892A pdb=" N ASP A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.714A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.020A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.950A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.510A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.574A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.636A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 441' Processing helix chain 'A' and resid 441 through 461 removed outlier: 4.237A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 3.627A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.683A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 3.830A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.771A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.047A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 removed outlier: 4.010A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.710A pdb=" N VAL D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 91 through 107 Proline residue: D 97 - end of helix removed outlier: 3.528A pdb=" N ILE D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.581A pdb=" N TYR D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 135 through 166 removed outlier: 3.778A pdb=" N ILE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 143 " --> pdb=" O TYR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.890A pdb=" N ASP D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 234 through 253 Processing helix chain 'D' and resid 262 through 267 removed outlier: 3.718A pdb=" N THR D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.021A pdb=" N GLY D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 304 through 320 removed outlier: 3.951A pdb=" N TRP D 308 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 338 through 373 removed outlier: 3.508A pdb=" N ASP D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 398 Proline residue: D 392 - end of helix Processing helix chain 'D' and resid 400 through 435 removed outlier: 3.572A pdb=" N TRP D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 441 removed outlier: 3.635A pdb=" N LYS D 439 " --> pdb=" O PHE D 435 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 435 through 441' Processing helix chain 'D' and resid 441 through 461 removed outlier: 4.250A pdb=" N PHE D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 494 removed outlier: 3.624A pdb=" N VAL D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 510 removed outlier: 3.676A pdb=" N PHE D 501 " --> pdb=" O GLY D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 523 Processing helix chain 'D' and resid 523 through 539 Processing helix chain 'D' and resid 551 through 580 removed outlier: 3.831A pdb=" N ASN D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Proline residue: D 570 - end of helix Processing helix chain 'D' and resid 583 through 592 Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.772A pdb=" N ALA D 602 " --> pdb=" O HIS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 removed outlier: 4.046A pdb=" N TRP D 614 " --> pdb=" O GLN D 610 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1680 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: 1.45 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2646 1.34 - 1.46: 2361 1.46 - 1.58: 4237 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9306 Sorted by residual: bond pdb=" CAJ E5E D 701 " pdb=" OAC E5E D 701 " ideal model delta sigma weight residual 1.350 1.401 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CAJ E5E A 701 " pdb=" OAC E5E A 701 " ideal model delta sigma weight residual 1.350 1.394 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" CAI E5E A 701 " pdb=" OAB E5E A 701 " ideal model delta sigma weight residual 1.354 1.395 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" CAI E5E D 701 " pdb=" OAB E5E D 701 " ideal model delta sigma weight residual 1.354 1.394 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" CAI E5E A 701 " pdb=" CAJ E5E A 701 " ideal model delta sigma weight residual 1.401 1.364 0.037 2.00e-02 2.50e+03 3.48e+00 ... (remaining 9301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 12455 1.72 - 3.43: 194 3.43 - 5.15: 34 5.15 - 6.87: 11 6.87 - 8.59: 2 Bond angle restraints: 12696 Sorted by residual: angle pdb=" C ASP A 546 " pdb=" CA ASP A 546 " pdb=" CB ASP A 546 " ideal model delta sigma weight residual 110.92 115.72 -4.80 1.59e+00 3.96e-01 9.11e+00 angle pdb=" C ASP D 546 " pdb=" CA ASP D 546 " pdb=" CB ASP D 546 " ideal model delta sigma weight residual 110.92 115.68 -4.76 1.59e+00 3.96e-01 8.98e+00 angle pdb=" N GLY D 231 " pdb=" CA GLY D 231 " pdb=" C GLY D 231 " ideal model delta sigma weight residual 111.21 114.29 -3.08 1.04e+00 9.25e-01 8.75e+00 angle pdb=" N GLY A 231 " pdb=" CA GLY A 231 " pdb=" C GLY A 231 " ideal model delta sigma weight residual 111.21 114.27 -3.06 1.04e+00 9.25e-01 8.65e+00 angle pdb=" C GLY D 106 " pdb=" N MET D 107 " pdb=" CA MET D 107 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.44e+00 1.68e-01 7.89e+00 ... (remaining 12691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4918 17.89 - 35.77: 210 35.77 - 53.66: 56 53.66 - 71.55: 6 71.55 - 89.43: 6 Dihedral angle restraints: 5196 sinusoidal: 1950 harmonic: 3246 Sorted by residual: dihedral pdb=" CA THR D 268 " pdb=" C THR D 268 " pdb=" N LEU D 269 " pdb=" CA LEU D 269 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA THR A 268 " pdb=" C THR A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER A 493 " pdb=" C SER A 493 " pdb=" N TRP A 494 " pdb=" CA TRP A 494 " ideal model delta harmonic sigma weight residual 180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1046 0.036 - 0.072: 304 0.072 - 0.108: 52 0.108 - 0.145: 9 0.145 - 0.181: 3 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CAL E5E D 701 " pdb=" CAH E5E D 701 " pdb=" CAK E5E D 701 " pdb=" OAD E5E D 701 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA LEU A 269 " pdb=" N LEU A 269 " pdb=" C LEU A 269 " pdb=" CB LEU A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA LEU D 269 " pdb=" N LEU D 269 " pdb=" C LEU D 269 " pdb=" CB LEU D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1411 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 477 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C ALA A 477 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA A 477 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 478 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 477 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ALA D 477 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA D 477 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 478 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 481 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ILE D 481 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE D 481 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 482 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2584 2.80 - 3.50: 13256 3.50 - 4.20: 21664 4.20 - 4.90: 39302 Nonbonded interactions: 76808 Sorted by model distance: nonbonded pdb=" OD1 ASN A 78 " pdb="NA NA A 703 " model vdw 1.402 3.210 nonbonded pdb=" OD1 ASN A 350 " pdb="NA NA A 703 " model vdw 2.088 3.210 nonbonded pdb=" OH TYR D 98 " pdb="CL CL D 702 " model vdw 2.113 3.270 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 702 " model vdw 2.161 3.270 nonbonded pdb=" OH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 2.216 3.040 ... (remaining 76803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.070 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 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 : 0.014 0.810 9309 Z= 1.379 Angle : 0.589 8.585 12696 Z= 0.342 Chirality : 0.036 0.181 1414 Planarity : 0.006 0.060 1544 Dihedral : 11.301 89.435 3132 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 6.75 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.89 (0.23), residues: 1120 helix: -0.91 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 442 TYR 0.024 0.001 TYR D 151 PHE 0.014 0.001 PHE D 65 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 ( 9306) covalent geometry : angle 0.58886 / 0.34 (12696) hydrogen bonds : bond 0.16661 / 10.95 ( 572) hydrogen bonds : angle 6.83494 / 4.70 ( 1680) Misc. bond : bond 0.76347 / 38.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: A 303 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7796 (mmtt) REVERT: A 377 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6497 (mm-30) REVERT: A 519 LEU cc_start: 0.8096 (mt) cc_final: 0.7734 (mt) REVERT: A 544 THR cc_start: 0.7115 (t) cc_final: 0.6758 (t) REVERT: A 548 TYR cc_start: 0.7364 (t80) cc_final: 0.6795 (t80) REVERT: A 563 LEU cc_start: 0.7006 (mt) cc_final: 0.6767 (mt) REVERT: A 615 LEU cc_start: 0.8194 (tt) cc_final: 0.7948 (mt) REVERT: D 107 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.3819 (mpp) REVERT: D 120 ASN cc_start: 0.8215 (m-40) cc_final: 0.7924 (m110) REVERT: D 133 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: D 303 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7778 (mmtt) REVERT: D 377 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6568 (mm-30) REVERT: D 515 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (tp) REVERT: D 519 LEU cc_start: 0.8130 (mt) cc_final: 0.7787 (mt) REVERT: D 544 THR cc_start: 0.7061 (t) cc_final: 0.6708 (t) REVERT: D 548 TYR cc_start: 0.7357 (t80) cc_final: 0.6860 (t80) REVERT: D 563 LEU cc_start: 0.7027 (mt) cc_final: 0.6782 (mt) REVERT: D 615 LEU cc_start: 0.8209 (tt) cc_final: 0.7971 (mt) outliers start: 42 outliers final: 6 residues processed: 309 average time/residue: 0.0776 time to fit residues: 34.0806 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 515 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 184 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 599 HIS A 610 GLN D 89 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 333 ASN D 599 HIS D 610 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163920 restraints weight = 12234.707| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.52 r_work: 0.3862 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9309 Z= 0.169 Angle : 0.608 7.740 12696 Z= 0.316 Chirality : 0.040 0.172 1414 Planarity : 0.005 0.058 1544 Dihedral : 5.823 49.594 1245 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.54 % Allowed : 13.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1120 helix: 0.35 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 341 TYR 0.019 0.002 TYR A 152 PHE 0.036 0.002 PHE D 359 TRP 0.010 0.001 TRP D 80 HIS 0.016 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 9306) covalent geometry : angle 0.60834 / 0.32 (12696) hydrogen bonds : bond 0.05124 / 3.48 ( 572) hydrogen bonds : angle 4.98097 / 3.47 ( 1680) Misc. bond : bond 0.00783 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.290 Fit side-chains REVERT: A 122 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7530 (mp0) REVERT: A 133 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: A 189 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6630 (tptt) REVERT: A 303 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7744 (mmtt) REVERT: A 367 TYR cc_start: 0.7763 (t80) cc_final: 0.7426 (t80) REVERT: A 377 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6818 (mm-30) REVERT: A 519 LEU cc_start: 0.8433 (mt) cc_final: 0.8199 (mt) REVERT: A 548 TYR cc_start: 0.7863 (t80) cc_final: 0.6881 (t80) REVERT: A 563 LEU cc_start: 0.7443 (mt) cc_final: 0.7186 (mt) REVERT: A 615 LEU cc_start: 0.8112 (tt) cc_final: 0.7826 (mt) REVERT: D 120 ASN cc_start: 0.8555 (m-40) cc_final: 0.7586 (m-40) REVERT: D 122 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7499 (mp0) REVERT: D 133 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: D 303 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7737 (mmtt) REVERT: D 332 TYR cc_start: 0.7820 (m-80) cc_final: 0.7553 (m-80) REVERT: D 367 TYR cc_start: 0.7697 (t80) cc_final: 0.7309 (t80) REVERT: D 377 GLU cc_start: 0.7638 (mt-10) cc_final: 0.6808 (mm-30) REVERT: D 519 LEU cc_start: 0.8542 (mt) cc_final: 0.8285 (mt) REVERT: D 548 TYR cc_start: 0.7787 (t80) cc_final: 0.6837 (t80) REVERT: D 563 LEU cc_start: 0.7467 (mt) cc_final: 0.7189 (mt) REVERT: D 615 LEU cc_start: 0.8134 (tt) cc_final: 0.7854 (mt) outliers start: 43 outliers final: 24 residues processed: 216 average time/residue: 0.0645 time to fit residues: 21.0133 Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 57 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN D 78 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160621 restraints weight = 12160.419| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.48 r_work: 0.3829 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9309 Z= 0.130 Angle : 0.536 6.492 12696 Z= 0.274 Chirality : 0.038 0.153 1414 Planarity : 0.004 0.047 1544 Dihedral : 5.306 50.634 1234 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.48 % Allowed : 16.35 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1120 helix: 0.73 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 341 TYR 0.017 0.001 TYR A 151 PHE 0.015 0.001 PHE D 65 TRP 0.008 0.001 TRP D 559 HIS 0.008 0.001 HIS D 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9306) covalent geometry : angle 0.53649 / 0.27 (12696) hydrogen bonds : bond 0.04696 / 3.16 ( 572) hydrogen bonds : angle 4.84148 / 3.36 ( 1680) Misc. bond : bond 0.00487 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8569 (pttt) cc_final: 0.8346 (ptpt) REVERT: A 122 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7603 (mp0) REVERT: A 133 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: A 189 LYS cc_start: 0.7355 (ttpt) cc_final: 0.6613 (tptt) REVERT: A 303 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7723 (mmtt) REVERT: A 367 TYR cc_start: 0.7898 (t80) cc_final: 0.7539 (t80) REVERT: A 377 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6835 (mm-30) REVERT: A 563 LEU cc_start: 0.7555 (mt) cc_final: 0.7268 (mt) REVERT: A 615 LEU cc_start: 0.8096 (tt) cc_final: 0.7843 (mt) REVERT: D 120 ASN cc_start: 0.8398 (m-40) cc_final: 0.7352 (m110) REVERT: D 122 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7559 (mp0) REVERT: D 133 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: D 303 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7696 (mmtt) REVERT: D 367 TYR cc_start: 0.7793 (t80) cc_final: 0.7436 (t80) REVERT: D 377 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6846 (mm-30) REVERT: D 519 LEU cc_start: 0.8555 (mt) cc_final: 0.8292 (mt) REVERT: D 563 LEU cc_start: 0.7577 (mt) cc_final: 0.7269 (mt) REVERT: D 584 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6906 (tt) REVERT: D 615 LEU cc_start: 0.8095 (tt) cc_final: 0.7857 (mt) outliers start: 33 outliers final: 23 residues processed: 198 average time/residue: 0.0648 time to fit residues: 19.1014 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 280 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 280 HIS D 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142689 restraints weight = 12335.591| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.54 r_work: 0.3619 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9309 Z= 0.184 Angle : 0.619 7.944 12696 Z= 0.317 Chirality : 0.041 0.184 1414 Planarity : 0.004 0.042 1544 Dihedral : 5.297 47.152 1234 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.43 % Allowed : 15.82 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1120 helix: 0.85 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 518 TYR 0.017 0.002 TYR D 572 PHE 0.023 0.002 PHE A 540 TRP 0.011 0.001 TRP A 559 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 9306) covalent geometry : angle 0.61878 / 0.32 (12696) hydrogen bonds : bond 0.05559 / 3.69 ( 572) hydrogen bonds : angle 5.18603 / 3.65 ( 1680) Misc. bond : bond 0.00579 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: A 189 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6555 (tptt) REVERT: A 303 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7682 (mmtt) REVERT: A 367 TYR cc_start: 0.8030 (t80) cc_final: 0.7593 (t80) REVERT: A 377 GLU cc_start: 0.7924 (mt-10) cc_final: 0.6944 (mm-30) REVERT: A 473 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6370 (t0) REVERT: A 508 MET cc_start: 0.8640 (mtp) cc_final: 0.8292 (mtp) REVERT: A 548 TYR cc_start: 0.8173 (t80) cc_final: 0.7916 (t80) REVERT: A 586 GLU cc_start: 0.7121 (tt0) cc_final: 0.6890 (tt0) REVERT: A 615 LEU cc_start: 0.8105 (tt) cc_final: 0.7832 (mt) REVERT: D 133 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: D 189 LYS cc_start: 0.7389 (ttpt) cc_final: 0.6632 (tptt) REVERT: D 303 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7677 (mmtt) REVERT: D 367 TYR cc_start: 0.7961 (t80) cc_final: 0.7525 (t80) REVERT: D 377 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7005 (mm-30) REVERT: D 473 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.5319 (t0) REVERT: D 584 LEU cc_start: 0.7505 (mm) cc_final: 0.6903 (tt) REVERT: D 615 LEU cc_start: 0.8129 (tt) cc_final: 0.7832 (mt) outliers start: 42 outliers final: 27 residues processed: 192 average time/residue: 0.0726 time to fit residues: 20.6845 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145430 restraints weight = 12374.595| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.50 r_work: 0.3660 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9309 Z= 0.143 Angle : 0.560 8.248 12696 Z= 0.287 Chirality : 0.039 0.163 1414 Planarity : 0.004 0.037 1544 Dihedral : 5.182 48.112 1230 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.01 % Allowed : 16.77 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1120 helix: 0.95 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.018 0.001 TYR D 151 PHE 0.015 0.001 PHE D 65 TRP 0.010 0.001 TRP D 517 HIS 0.004 0.001 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9306) covalent geometry : angle 0.55995 / 0.29 (12696) hydrogen bonds : bond 0.05085 / 3.40 ( 572) hydrogen bonds : angle 5.01525 / 3.52 ( 1680) Misc. bond : bond 0.00443 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7609 (mp0) REVERT: A 133 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: A 189 LYS cc_start: 0.7299 (ttpt) cc_final: 0.6499 (tptt) REVERT: A 303 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7696 (mmtt) REVERT: A 377 GLU cc_start: 0.7907 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 473 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.5460 (t0) REVERT: A 519 LEU cc_start: 0.8670 (mt) cc_final: 0.8430 (mt) REVERT: A 597 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 615 LEU cc_start: 0.8082 (tt) cc_final: 0.7787 (mt) REVERT: D 122 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7603 (mp0) REVERT: D 133 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8586 (m-80) REVERT: D 303 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7670 (mmtt) REVERT: D 367 TYR cc_start: 0.8009 (t80) cc_final: 0.7577 (t80) REVERT: D 377 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7053 (mm-30) REVERT: D 473 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.5451 (t70) REVERT: D 519 LEU cc_start: 0.8679 (mt) cc_final: 0.8444 (mt) REVERT: D 584 LEU cc_start: 0.7519 (mm) cc_final: 0.6922 (tt) REVERT: D 586 GLU cc_start: 0.7078 (tt0) cc_final: 0.6850 (tt0) REVERT: D 615 LEU cc_start: 0.8139 (tt) cc_final: 0.7850 (mt) outliers start: 38 outliers final: 26 residues processed: 189 average time/residue: 0.0692 time to fit residues: 19.2280 Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140733 restraints weight = 12404.121| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.47 r_work: 0.3595 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9309 Z= 0.154 Angle : 0.571 6.451 12696 Z= 0.295 Chirality : 0.039 0.169 1414 Planarity : 0.004 0.035 1544 Dihedral : 5.239 50.730 1230 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.43 % Allowed : 16.77 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1120 helix: 0.95 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.41 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.016 0.001 TYR D 151 PHE 0.016 0.001 PHE A 65 TRP 0.007 0.001 TRP A 517 HIS 0.007 0.001 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9306) covalent geometry : angle 0.57120 / 0.30 (12696) hydrogen bonds : bond 0.05257 / 3.48 ( 572) hydrogen bonds : angle 5.04333 / 3.55 ( 1680) Misc. bond : bond 0.00490 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7606 (mp0) REVERT: A 133 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: A 189 LYS cc_start: 0.7277 (ttpt) cc_final: 0.6476 (tptt) REVERT: A 303 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7696 (mmtt) REVERT: A 367 TYR cc_start: 0.8030 (t80) cc_final: 0.7636 (t80) REVERT: A 377 GLU cc_start: 0.7923 (mt-10) cc_final: 0.6983 (mm-30) REVERT: A 473 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6009 (t0) REVERT: A 597 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 615 LEU cc_start: 0.8206 (tt) cc_final: 0.7890 (mt) REVERT: D 122 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7599 (mp0) REVERT: D 133 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: D 184 ASN cc_start: 0.6986 (m-40) cc_final: 0.6695 (m110) REVERT: D 303 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7686 (mmtt) REVERT: D 377 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7036 (mm-30) REVERT: D 584 LEU cc_start: 0.7507 (mm) cc_final: 0.6912 (tt) REVERT: D 615 LEU cc_start: 0.8106 (tt) cc_final: 0.7822 (mt) outliers start: 42 outliers final: 28 residues processed: 171 average time/residue: 0.0698 time to fit residues: 17.4500 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141468 restraints weight = 12453.409| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.47 r_work: 0.3606 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9309 Z= 0.145 Angle : 0.557 5.621 12696 Z= 0.289 Chirality : 0.039 0.166 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.190 50.367 1230 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.38 % Allowed : 16.77 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1120 helix: 1.07 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 216 TYR 0.020 0.001 TYR D 151 PHE 0.016 0.001 PHE A 65 TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9306) covalent geometry : angle 0.55699 / 0.29 (12696) hydrogen bonds : bond 0.05164 / 3.44 ( 572) hydrogen bonds : angle 5.04919 / 3.56 ( 1680) Misc. bond : bond 0.00449 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7580 (mp0) REVERT: A 133 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: A 189 LYS cc_start: 0.7280 (ttpt) cc_final: 0.6480 (tptt) REVERT: A 303 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7698 (mmtt) REVERT: A 342 ASP cc_start: 0.8228 (t0) cc_final: 0.7897 (t0) REVERT: A 367 TYR cc_start: 0.8068 (t80) cc_final: 0.7670 (t80) REVERT: A 377 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 473 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.5846 (t0) REVERT: A 597 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 615 LEU cc_start: 0.8089 (tt) cc_final: 0.7801 (mt) REVERT: D 122 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7584 (mp0) REVERT: D 133 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: D 303 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7681 (mmtt) REVERT: D 342 ASP cc_start: 0.8208 (t0) cc_final: 0.7881 (t0) REVERT: D 367 TYR cc_start: 0.8048 (t80) cc_final: 0.7646 (t80) REVERT: D 377 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7055 (mm-30) REVERT: D 584 LEU cc_start: 0.7515 (mm) cc_final: 0.6929 (tt) REVERT: D 615 LEU cc_start: 0.8101 (tt) cc_final: 0.7820 (mt) outliers start: 32 outliers final: 28 residues processed: 171 average time/residue: 0.0669 time to fit residues: 16.8404 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143310 restraints weight = 12375.282| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.46 r_work: 0.3633 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9309 Z= 0.133 Angle : 0.545 5.745 12696 Z= 0.282 Chirality : 0.038 0.170 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.184 52.220 1230 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.48 % Allowed : 16.98 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1120 helix: 1.14 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.49 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.032 0.001 TYR D 151 PHE 0.042 0.001 PHE A 213 TRP 0.007 0.001 TRP A 235 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9306) covalent geometry : angle 0.54458 / 0.28 (12696) hydrogen bonds : bond 0.04911 / 3.28 ( 572) hydrogen bonds : angle 4.96321 / 3.49 ( 1680) Misc. bond : bond 0.00393 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7575 (mp0) REVERT: A 133 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: A 165 SER cc_start: 0.8835 (m) cc_final: 0.8547 (t) REVERT: A 184 ASN cc_start: 0.6767 (m110) cc_final: 0.6554 (m110) REVERT: A 234 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7446 (mm-40) REVERT: A 303 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7701 (mmtt) REVERT: A 342 ASP cc_start: 0.8202 (t0) cc_final: 0.7895 (t0) REVERT: A 367 TYR cc_start: 0.8057 (t80) cc_final: 0.7664 (t80) REVERT: A 377 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7105 (mm-30) REVERT: A 473 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.5640 (t0) REVERT: A 597 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 615 LEU cc_start: 0.8072 (tt) cc_final: 0.7786 (mt) REVERT: D 122 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7583 (mp0) REVERT: D 133 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8644 (m-80) REVERT: D 184 ASN cc_start: 0.6769 (m110) cc_final: 0.6517 (m110) REVERT: D 303 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7714 (mmtt) REVERT: D 342 ASP cc_start: 0.8173 (t0) cc_final: 0.7844 (t0) REVERT: D 367 TYR cc_start: 0.8094 (t80) cc_final: 0.7704 (t80) REVERT: D 377 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7019 (mm-30) REVERT: D 473 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.5801 (t0) REVERT: D 584 LEU cc_start: 0.7490 (mm) cc_final: 0.6892 (tt) REVERT: D 615 LEU cc_start: 0.8067 (tt) cc_final: 0.7792 (mt) outliers start: 33 outliers final: 25 residues processed: 171 average time/residue: 0.0682 time to fit residues: 17.3490 Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141475 restraints weight = 12461.228| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.49 r_work: 0.3607 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9309 Z= 0.144 Angle : 0.564 6.216 12696 Z= 0.292 Chirality : 0.039 0.188 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.204 53.306 1230 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 18.35 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1120 helix: 1.13 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.52 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.030 0.001 TYR D 151 PHE 0.032 0.001 PHE A 213 TRP 0.012 0.001 TRP D 235 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9306) covalent geometry : angle 0.56353 / 0.29 (12696) hydrogen bonds : bond 0.05052 / 3.37 ( 572) hydrogen bonds : angle 5.04576 / 3.55 ( 1680) Misc. bond : bond 0.00430 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.227 Fit side-chains REVERT: A 122 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7586 (mp0) REVERT: A 133 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8658 (m-80) REVERT: A 184 ASN cc_start: 0.6878 (m110) cc_final: 0.6606 (m110) REVERT: A 303 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7710 (mmtt) REVERT: A 342 ASP cc_start: 0.8217 (t0) cc_final: 0.7903 (t0) REVERT: A 367 TYR cc_start: 0.8106 (t80) cc_final: 0.7713 (t80) REVERT: A 377 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7059 (mm-30) REVERT: A 473 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.5977 (t0) REVERT: A 597 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 615 LEU cc_start: 0.8075 (tt) cc_final: 0.7790 (mt) REVERT: D 122 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7583 (mp0) REVERT: D 133 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: D 303 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7713 (mmtt) REVERT: D 342 ASP cc_start: 0.8187 (t0) cc_final: 0.7847 (t0) REVERT: D 367 TYR cc_start: 0.8076 (t80) cc_final: 0.7667 (t80) REVERT: D 377 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7113 (mm-30) REVERT: D 584 LEU cc_start: 0.7481 (mm) cc_final: 0.6886 (tt) REVERT: D 615 LEU cc_start: 0.8070 (tt) cc_final: 0.7795 (mt) outliers start: 30 outliers final: 24 residues processed: 169 average time/residue: 0.0692 time to fit residues: 17.4020 Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 184 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139898 restraints weight = 12377.275| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.48 r_work: 0.3587 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9309 Z= 0.150 Angle : 0.579 6.070 12696 Z= 0.299 Chirality : 0.040 0.181 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.205 52.508 1230 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.38 % Allowed : 18.46 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1120 helix: 1.09 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 216 TYR 0.029 0.001 TYR D 151 PHE 0.029 0.001 PHE A 213 TRP 0.008 0.001 TRP D 235 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9306) covalent geometry : angle 0.57861 / 0.30 (12696) hydrogen bonds : bond 0.05166 / 3.45 ( 572) hydrogen bonds : angle 5.07462 / 3.57 ( 1680) Misc. bond : bond 0.00447 / 0.23 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.356 Fit side-chains REVERT: A 133 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: A 184 ASN cc_start: 0.6887 (m110) cc_final: 0.6658 (m110) REVERT: A 303 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7703 (mmtt) REVERT: A 342 ASP cc_start: 0.8196 (t0) cc_final: 0.7873 (t0) REVERT: A 367 TYR cc_start: 0.8169 (t80) cc_final: 0.7768 (t80) REVERT: A 377 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7149 (mm-30) REVERT: A 473 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6195 (t0) REVERT: A 597 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 615 LEU cc_start: 0.8110 (tt) cc_final: 0.7824 (mt) REVERT: D 133 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: D 184 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.5948 (p0) REVERT: D 303 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7716 (mmtt) REVERT: D 342 ASP cc_start: 0.8174 (t0) cc_final: 0.7819 (t0) REVERT: D 367 TYR cc_start: 0.8141 (t80) cc_final: 0.7732 (t80) REVERT: D 377 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7118 (mm-30) REVERT: D 473 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6161 (t0) REVERT: D 584 LEU cc_start: 0.7435 (mm) cc_final: 0.6851 (tt) REVERT: D 615 LEU cc_start: 0.8066 (tt) cc_final: 0.7787 (mt) outliers start: 32 outliers final: 26 residues processed: 161 average time/residue: 0.0686 time to fit residues: 16.6630 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.0000 chunk 51 optimal weight: 0.0050 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** D 220 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.174739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142577 restraints weight = 12228.729| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.45 r_work: 0.3622 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9309 Z= 0.135 Angle : 0.569 7.290 12696 Z= 0.293 Chirality : 0.039 0.186 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.169 51.838 1230 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1120 helix: 1.14 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.54 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 216 TYR 0.031 0.001 TYR D 151 PHE 0.030 0.001 PHE A 213 TRP 0.009 0.001 TRP D 235 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9306) covalent geometry : angle 0.56853 / 0.29 (12696) hydrogen bonds : bond 0.04940 / 3.31 ( 572) hydrogen bonds : angle 5.00399 / 3.51 ( 1680) Misc. bond : bond 0.00382 / 0.20 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.10 seconds wall clock time: 31 minutes 9.57 seconds (1869.57 seconds total)