Starting phenix.real_space_refine on Wed Sep 17 13:48:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y95_39070/09_2025/8y95_39070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y95_39070/09_2025/8y95_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_39070/09_2025/8y95_39070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y95_39070/09_2025/8y95_39070.map" model { file = "/net/cci-nas-00/data/ceres_data/8y95_39070/09_2025/8y95_39070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y95_39070/09_2025/8y95_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-2.0-5805/lib/python3.9/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, 14 Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CL': 1, ' NA': 1, 'E5E': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.17, per 1000 atoms: 0.24 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: 0.85 Conformation dependent library (CDL) restraints added in 281.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 1.44 Time building geometry restraints manager: 1.06 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 2.470 nonbonded pdb=" OD1 ASN A 350 " pdb="NA NA A 703 " model vdw 2.088 2.470 nonbonded pdb=" OH TYR D 98 " pdb="CL CL D 702 " model vdw 2.113 3.190 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 702 " model vdw 2.161 3.190 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.150 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 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 aren 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 covalent geometry : bond 0.00253 ( 9306) covalent geometry : angle 0.58886 (12696) hydrogen bonds : bond 0.16661 ( 572) hydrogen bonds : angle 6.83494 ( 1680) Misc. bond : bond 0.76347 ( 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 : 0.378 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: 0.7356 (t80) cc_final: 0.6860 (t80) REVERT: D 563 LEU cc_start: 0.7028 (mt) cc_final: 0.6783 (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: 0.0902 time to fit residues: 39.0192 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 : 0.249 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 350 ASN D 599 HIS D 610 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.191947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163799 restraints weight = 12220.788| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.51 r_work: 0.3861 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9309 Z= 0.164 Angle : 0.595 7.438 12696 Z= 0.308 Chirality : 0.040 0.163 1414 Planarity : 0.005 0.058 1544 Dihedral : 5.787 49.905 1245 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.32 % Allowed : 13.82 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.25), residues: 1120 helix: 0.31 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.019 0.002 TYR A 151 PHE 0.035 0.002 PHE A 359 TRP 0.010 0.001 TRP D 80 HIS 0.014 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9306) covalent geometry : angle 0.59506 (12696) hydrogen bonds : bond 0.05215 ( 572) hydrogen bonds : angle 4.97613 ( 1680) Misc. bond : bond 0.00756 ( 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 225 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.337 Fit side-chains REVERT: A 122 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7553 (mp0) REVERT: A 133 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: A 189 LYS cc_start: 0.7330 (ttpt) cc_final: 0.6601 (tptt) REVERT: A 303 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7746 (mmtt) REVERT: A 367 TYR cc_start: 0.7768 (t80) cc_final: 0.7458 (t80) REVERT: A 377 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6827 (mm-30) REVERT: A 519 LEU cc_start: 0.8433 (mt) cc_final: 0.8202 (mt) REVERT: A 548 TYR cc_start: 0.7876 (t80) cc_final: 0.6897 (t80) REVERT: A 563 LEU cc_start: 0.7452 (mt) cc_final: 0.7191 (mt) REVERT: A 606 ILE cc_start: 0.6800 (mp) cc_final: 0.6462 (mp) REVERT: A 609 PHE cc_start: 0.8113 (m-10) cc_final: 0.7851 (m-80) REVERT: A 615 LEU cc_start: 0.8119 (tt) cc_final: 0.7834 (mt) REVERT: D 107 MET cc_start: 0.5795 (mpp) cc_final: 0.5407 (mmp) REVERT: D 120 ASN cc_start: 0.8528 (m-40) cc_final: 0.7548 (m-40) REVERT: D 122 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7541 (mp0) REVERT: D 133 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: D 303 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7738 (mmtt) REVERT: D 332 TYR cc_start: 0.7826 (m-80) cc_final: 0.7549 (m-80) REVERT: D 367 TYR cc_start: 0.7709 (t80) cc_final: 0.7390 (t80) REVERT: D 377 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6836 (mm-30) REVERT: D 517 TRP cc_start: 0.7631 (m100) cc_final: 0.7395 (m100) REVERT: D 519 LEU cc_start: 0.8548 (mt) cc_final: 0.8290 (mt) REVERT: D 548 TYR cc_start: 0.7839 (t80) cc_final: 0.6884 (t80) REVERT: D 563 LEU cc_start: 0.7473 (mt) cc_final: 0.7195 (mt) REVERT: D 615 LEU cc_start: 0.8139 (tt) cc_final: 0.7860 (mt) outliers start: 41 outliers final: 25 residues processed: 217 average time/residue: 0.0734 time to fit residues: 23.8807 Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 419 SER 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: 0.0050 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 57 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.9206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** 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 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.181585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150749 restraints weight = 12185.285| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.46 r_work: 0.3714 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9309 Z= 0.153 Angle : 0.567 6.917 12696 Z= 0.293 Chirality : 0.040 0.159 1414 Planarity : 0.004 0.047 1544 Dihedral : 5.306 48.615 1234 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 aren not related in a simple way. whole: 0.32 (0.25), residues: 1120 helix: 0.66 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.021 0.002 TYR D 572 PHE 0.017 0.002 PHE D 65 TRP 0.011 0.001 TRP A 559 HIS 0.009 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9306) covalent geometry : angle 0.56680 (12696) hydrogen bonds : bond 0.05134 ( 572) hydrogen bonds : angle 4.99031 ( 1680) Misc. bond : bond 0.00647 ( 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 201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.274 Fit side-chains REVERT: A 133 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: A 189 LYS cc_start: 0.7389 (ttpt) cc_final: 0.6625 (tptt) REVERT: A 303 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7684 (mmtt) REVERT: A 367 TYR cc_start: 0.7998 (t80) cc_final: 0.7605 (t80) REVERT: A 377 GLU cc_start: 0.7825 (mt-10) cc_final: 0.6892 (mm-30) REVERT: A 473 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.4639 (t0) REVERT: A 563 LEU cc_start: 0.7852 (mt) cc_final: 0.7613 (mt) REVERT: A 615 LEU cc_start: 0.8084 (tt) cc_final: 0.7832 (mt) REVERT: D 88 LYS cc_start: 0.8685 (pttt) cc_final: 0.8478 (ptpt) REVERT: D 107 MET cc_start: 0.6181 (mpp) cc_final: 0.5885 (mmt) REVERT: D 133 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: D 303 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7660 (mmtt) REVERT: D 367 TYR cc_start: 0.7961 (t80) cc_final: 0.7581 (t80) REVERT: D 377 GLU cc_start: 0.7828 (mt-10) cc_final: 0.6948 (mm-30) REVERT: D 563 LEU cc_start: 0.7831 (mt) cc_final: 0.7602 (mt) REVERT: D 581 GLN cc_start: 0.7328 (tp40) cc_final: 0.7116 (tp40) REVERT: D 584 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6928 (tt) REVERT: D 586 GLU cc_start: 0.7092 (tt0) cc_final: 0.6842 (tt0) REVERT: D 615 LEU cc_start: 0.8100 (tt) cc_final: 0.7825 (mt) outliers start: 32 outliers final: 18 residues processed: 196 average time/residue: 0.0782 time to fit residues: 22.5976 Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 230 ILE 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 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 230 ILE Chi-restraints excluded: chain D residue 421 MET 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: 0.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 228 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 228 HIS ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147365 restraints weight = 12376.676| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.53 r_work: 0.3675 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9309 Z= 0.157 Angle : 0.570 6.659 12696 Z= 0.291 Chirality : 0.039 0.164 1414 Planarity : 0.004 0.044 1544 Dihedral : 5.191 46.827 1234 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.59 % Allowed : 17.51 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1120 helix: 0.87 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.022 0.001 TYR A 151 PHE 0.025 0.001 PHE D 540 TRP 0.009 0.001 TRP D 559 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9306) covalent geometry : angle 0.57040 (12696) hydrogen bonds : bond 0.05134 ( 572) hydrogen bonds : angle 5.04373 ( 1680) Misc. bond : bond 0.00489 ( 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 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7672 (mp0) REVERT: A 133 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: A 189 LYS cc_start: 0.7350 (ttpt) cc_final: 0.6557 (tptt) REVERT: A 303 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7712 (mmtt) REVERT: A 377 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6948 (mm-30) REVERT: A 473 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.5193 (t0) REVERT: A 548 TYR cc_start: 0.8222 (t80) cc_final: 0.7951 (t80) REVERT: A 586 GLU cc_start: 0.7109 (tt0) cc_final: 0.6873 (tt0) REVERT: A 615 LEU cc_start: 0.8097 (tt) cc_final: 0.7806 (mt) REVERT: D 122 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7619 (mp0) REVERT: D 133 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8555 (m-80) REVERT: D 303 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7706 (mmtt) REVERT: D 367 TYR cc_start: 0.7955 (t80) cc_final: 0.7530 (t80) REVERT: D 377 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7022 (mm-30) REVERT: D 548 TYR cc_start: 0.8216 (t80) cc_final: 0.7951 (t80) REVERT: D 581 GLN cc_start: 0.7323 (tp40) cc_final: 0.7121 (tp40) REVERT: D 584 LEU cc_start: 0.7567 (mm) cc_final: 0.6974 (tt) REVERT: D 586 GLU cc_start: 0.7085 (tt0) cc_final: 0.6861 (tt0) REVERT: D 615 LEU cc_start: 0.8166 (tt) cc_final: 0.7885 (mt) outliers start: 34 outliers final: 22 residues processed: 179 average time/residue: 0.0832 time to fit residues: 22.1033 Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER 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 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 280 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147876 restraints weight = 12387.662| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.50 r_work: 0.3686 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9309 Z= 0.133 Angle : 0.537 6.750 12696 Z= 0.276 Chirality : 0.038 0.162 1414 Planarity : 0.004 0.042 1544 Dihedral : 5.115 48.927 1230 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.27 % Allowed : 18.35 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1120 helix: 1.07 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.71 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 341 TYR 0.024 0.001 TYR A 151 PHE 0.015 0.001 PHE D 65 TRP 0.008 0.001 TRP D 517 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9306) covalent geometry : angle 0.53690 (12696) hydrogen bonds : bond 0.04887 ( 572) hydrogen bonds : angle 4.95435 ( 1680) Misc. bond : bond 0.00437 ( 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 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7606 (mp0) REVERT: A 133 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: A 189 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6483 (tptt) REVERT: A 303 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7695 (mmtt) REVERT: A 367 TYR cc_start: 0.7886 (t80) cc_final: 0.7480 (t80) REVERT: A 377 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7074 (mm-30) REVERT: A 473 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.4963 (t0) REVERT: A 597 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 615 LEU cc_start: 0.8107 (tt) cc_final: 0.7817 (mt) REVERT: D 107 MET cc_start: 0.6791 (mmt) cc_final: 0.6590 (mmm) REVERT: D 122 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7602 (mp0) REVERT: D 133 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: D 303 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7693 (mmtt) REVERT: D 367 TYR cc_start: 0.8027 (t80) cc_final: 0.7604 (t80) REVERT: D 377 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7025 (mm-30) REVERT: D 473 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5159 (t0) REVERT: D 548 TYR cc_start: 0.8220 (t80) cc_final: 0.7943 (t80) REVERT: D 584 LEU cc_start: 0.7530 (mm) cc_final: 0.6953 (tt) REVERT: D 586 GLU cc_start: 0.7055 (tt0) cc_final: 0.6844 (tt0) REVERT: D 615 LEU cc_start: 0.8111 (tt) cc_final: 0.7837 (mt) outliers start: 31 outliers final: 20 residues processed: 179 average time/residue: 0.0900 time to fit residues: 23.4315 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL 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 268 THR Chi-restraints excluded: chain D residue 344 LEU 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 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 333 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142543 restraints weight = 12391.580| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.50 r_work: 0.3626 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9309 Z= 0.148 Angle : 0.559 6.801 12696 Z= 0.287 Chirality : 0.039 0.168 1414 Planarity : 0.004 0.038 1544 Dihedral : 5.110 49.937 1230 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.11 % Allowed : 17.83 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1120 helix: 1.00 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.65 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.022 0.001 TYR A 151 PHE 0.017 0.001 PHE A 65 TRP 0.010 0.001 TRP D 517 HIS 0.006 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9306) covalent geometry : angle 0.55909 (12696) hydrogen bonds : bond 0.05193 ( 572) hydrogen bonds : angle 5.05508 ( 1680) Misc. bond : bond 0.00483 ( 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 187 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7588 (mp0) REVERT: A 133 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: A 189 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6467 (tptt) REVERT: A 367 TYR cc_start: 0.8003 (t80) cc_final: 0.7590 (t80) REVERT: A 377 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7191 (mm-30) REVERT: A 473 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.5824 (t0) REVERT: A 615 LEU cc_start: 0.8086 (tt) cc_final: 0.7802 (mt) REVERT: D 107 MET cc_start: 0.6939 (mmt) cc_final: 0.6711 (mmm) REVERT: D 122 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7576 (mp0) REVERT: D 133 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: D 303 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7702 (mmtt) REVERT: D 377 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7068 (mm-30) REVERT: D 584 LEU cc_start: 0.7515 (mm) cc_final: 0.6949 (tt) REVERT: D 586 GLU cc_start: 0.7152 (tt0) cc_final: 0.6925 (tt0) REVERT: D 615 LEU cc_start: 0.8121 (tt) cc_final: 0.7834 (mt) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.0803 time to fit residues: 21.0461 Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 LEU 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 74 VAL 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 268 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 349 ILE 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 535 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: 0.6980 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 598 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.174651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142419 restraints weight = 12461.868| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.51 r_work: 0.3625 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9309 Z= 0.143 Angle : 0.548 5.501 12696 Z= 0.284 Chirality : 0.038 0.185 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.116 50.477 1230 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.38 % Allowed : 18.04 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1120 helix: 1.07 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 341 TYR 0.023 0.001 TYR A 151 PHE 0.016 0.001 PHE D 65 TRP 0.009 0.001 TRP D 517 HIS 0.004 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9306) covalent geometry : angle 0.54822 (12696) hydrogen bonds : bond 0.05061 ( 572) hydrogen bonds : angle 5.01830 ( 1680) Misc. bond : bond 0.00456 ( 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 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.354 Fit side-chains REVERT: A 122 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7589 (mp0) REVERT: A 133 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: A 184 ASN cc_start: 0.6934 (m-40) cc_final: 0.6653 (m110) REVERT: A 189 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6472 (tptt) REVERT: A 303 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7724 (mmtt) REVERT: A 342 ASP cc_start: 0.8215 (t0) cc_final: 0.7876 (t0) REVERT: A 367 TYR cc_start: 0.8049 (t80) cc_final: 0.7642 (t80) REVERT: A 377 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7059 (mm-30) REVERT: A 473 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.5680 (t0) REVERT: A 615 LEU cc_start: 0.8089 (tt) cc_final: 0.7805 (mt) REVERT: D 107 MET cc_start: 0.6911 (mmt) cc_final: 0.6691 (mmm) REVERT: D 133 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: D 184 ASN cc_start: 0.6933 (m-40) cc_final: 0.6670 (m110) REVERT: D 303 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7707 (mmtt) REVERT: D 342 ASP cc_start: 0.8170 (t0) cc_final: 0.7838 (t0) REVERT: D 367 TYR cc_start: 0.8001 (t80) cc_final: 0.7621 (t80) REVERT: D 377 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7006 (mm-30) REVERT: D 473 ASP cc_start: 0.6509 (OUTLIER) cc_final: 0.5192 (t70) REVERT: D 584 LEU cc_start: 0.7499 (mm) cc_final: 0.6912 (tt) REVERT: D 615 LEU cc_start: 0.8098 (tt) cc_final: 0.7817 (mt) outliers start: 32 outliers final: 23 residues processed: 168 average time/residue: 0.0817 time to fit residues: 20.2222 Evaluate side-chains 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 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 344 LEU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143737 restraints weight = 12413.456| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.48 r_work: 0.3636 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4914 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= 0.133 Angle : 0.541 5.735 12696 Z= 0.280 Chirality : 0.038 0.189 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.268 57.054 1230 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 18.14 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1120 helix: 1.12 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.63 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 216 TYR 0.024 0.001 TYR A 151 PHE 0.015 0.001 PHE D 65 TRP 0.012 0.001 TRP D 235 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9306) covalent geometry : angle 0.54080 (12696) hydrogen bonds : bond 0.04912 ( 572) hydrogen bonds : angle 4.99561 ( 1680) Misc. bond : bond 0.00425 ( 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 : 0.393 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: A 303 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7716 (mmtt) REVERT: A 342 ASP cc_start: 0.8199 (t0) cc_final: 0.7858 (t0) REVERT: A 367 TYR cc_start: 0.8063 (t80) cc_final: 0.7632 (t80) REVERT: A 377 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 434 ASP cc_start: 0.8267 (t0) cc_final: 0.8038 (t0) REVERT: A 444 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 473 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.5530 (t0) REVERT: A 615 LEU cc_start: 0.8084 (tt) cc_final: 0.7796 (mt) REVERT: D 107 MET cc_start: 0.6907 (mmt) cc_final: 0.6685 (mmm) REVERT: D 122 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7561 (mp0) REVERT: D 133 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: D 303 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7705 (mmtt) REVERT: D 342 ASP cc_start: 0.8159 (t0) cc_final: 0.7841 (t0) REVERT: D 367 TYR cc_start: 0.8050 (t80) cc_final: 0.7665 (t80) REVERT: D 377 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7066 (mm-30) REVERT: D 584 LEU cc_start: 0.7453 (mm) cc_final: 0.6868 (tt) REVERT: D 615 LEU cc_start: 0.8071 (tt) cc_final: 0.7793 (mt) outliers start: 33 outliers final: 22 residues processed: 173 average time/residue: 0.0823 time to fit residues: 20.8810 Evaluate side-chains 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 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 205 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET 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 535 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: 0.7980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143005 restraints weight = 12418.544| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.51 r_work: 0.3628 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5001 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= 0.141 Angle : 0.558 6.211 12696 Z= 0.290 Chirality : 0.040 0.223 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.302 58.118 1230 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 18.78 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1120 helix: 1.13 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.65 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 216 TYR 0.024 0.001 TYR A 151 PHE 0.044 0.001 PHE A 213 TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9306) covalent geometry : angle 0.55789 (12696) hydrogen bonds : bond 0.05001 ( 572) hydrogen bonds : angle 5.04975 ( 1680) Misc. bond : bond 0.00438 ( 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 174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7564 (mp0) REVERT: A 133 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: A 184 ASN cc_start: 0.6797 (m110) cc_final: 0.6544 (m110) REVERT: A 303 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7730 (mmtt) REVERT: A 342 ASP cc_start: 0.8196 (t0) cc_final: 0.7854 (t0) REVERT: A 367 TYR cc_start: 0.8121 (t80) cc_final: 0.7697 (t80) REVERT: A 377 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7153 (mm-30) REVERT: A 473 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.5733 (t0) REVERT: A 615 LEU cc_start: 0.8069 (tt) cc_final: 0.7791 (mt) REVERT: D 107 MET cc_start: 0.6927 (mmt) cc_final: 0.6706 (mmm) REVERT: D 122 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7584 (mp0) REVERT: D 133 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8686 (m-80) REVERT: D 184 ASN cc_start: 0.6809 (m110) cc_final: 0.6581 (m110) REVERT: D 303 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7727 (mmtt) REVERT: D 342 ASP cc_start: 0.8149 (t0) cc_final: 0.7829 (t0) REVERT: D 367 TYR cc_start: 0.8088 (t80) cc_final: 0.7702 (t80) REVERT: D 377 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7154 (mm-30) REVERT: D 471 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6715 (tp) REVERT: D 584 LEU cc_start: 0.7473 (mm) cc_final: 0.6888 (tt) REVERT: D 615 LEU cc_start: 0.8070 (tt) cc_final: 0.7794 (mt) outliers start: 30 outliers final: 24 residues processed: 166 average time/residue: 0.0842 time to fit residues: 20.4724 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 VAL 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 205 TYR 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 535 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: 0.0000 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144586 restraints weight = 12413.990| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.50 r_work: 0.3650 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5050 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= 0.133 Angle : 0.554 6.389 12696 Z= 0.288 Chirality : 0.039 0.192 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.316 58.869 1230 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 18.99 % Favored : 77.85 % 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 aren not related in a simple way. whole: 0.80 (0.25), residues: 1120 helix: 1.13 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.63 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.025 0.001 TYR A 151 PHE 0.041 0.001 PHE A 213 TRP 0.008 0.001 TRP D 517 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9306) covalent geometry : angle 0.55433 (12696) hydrogen bonds : bond 0.04882 ( 572) hydrogen bonds : angle 5.01538 ( 1680) Misc. bond : bond 0.00401 ( 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 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.6625 (m100) cc_final: 0.6323 (m100) REVERT: A 133 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: A 342 ASP cc_start: 0.8201 (t0) cc_final: 0.7886 (t0) REVERT: A 367 TYR cc_start: 0.8158 (t80) cc_final: 0.7733 (t80) REVERT: A 377 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7266 (mm-30) REVERT: A 434 ASP cc_start: 0.8267 (t0) cc_final: 0.8055 (t0) REVERT: A 473 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.5587 (t0) REVERT: A 615 LEU cc_start: 0.8071 (tt) cc_final: 0.7804 (mt) REVERT: D 107 MET cc_start: 0.6880 (mmt) cc_final: 0.6664 (mmm) REVERT: D 122 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7601 (mp0) REVERT: D 133 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: D 303 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7753 (mmtt) REVERT: D 342 ASP cc_start: 0.8169 (t0) cc_final: 0.7870 (t0) REVERT: D 367 TYR cc_start: 0.8086 (t80) cc_final: 0.7712 (t80) REVERT: D 377 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7134 (mm-30) REVERT: D 434 ASP cc_start: 0.8285 (t0) cc_final: 0.8053 (t0) REVERT: D 584 LEU cc_start: 0.7456 (mm) cc_final: 0.6892 (tt) REVERT: D 615 LEU cc_start: 0.8079 (tt) cc_final: 0.7817 (mt) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.0825 time to fit residues: 19.6131 Evaluate side-chains 163 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 419 SER Chi-restraints excluded: chain A residue 437 VAL 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 205 TYR 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 535 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 8 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 108 optimal weight: 0.0010 chunk 18 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146302 restraints weight = 12206.538| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.45 r_work: 0.3662 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5049 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= 0.128 Angle : 0.546 6.495 12696 Z= 0.283 Chirality : 0.039 0.184 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.323 59.657 1230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.38 % Allowed : 18.99 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1120 helix: 1.12 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.52 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 216 TYR 0.026 0.001 TYR A 151 PHE 0.039 0.001 PHE A 213 TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9306) covalent geometry : angle 0.54608 (12696) hydrogen bonds : bond 0.04690 ( 572) hydrogen bonds : angle 4.94716 ( 1680) Misc. bond : bond 0.00376 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.14 seconds wall clock time: 33 minutes 38.28 seconds (2018.28 seconds total)