Starting phenix.real_space_refine on Thu Jan 16 01:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y95_39070/01_2025/8y95_39070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y95_39070/01_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_39070/01_2025/8y95_39070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y95_39070/01_2025/8y95_39070.map" model { file = "/net/cci-nas-00/data/ceres_data/8y95_39070/01_2025/8y95_39070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y95_39070/01_2025/8y95_39070.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.68, per 1000 atoms: 0.63 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 2.53 Time building geometry restraints manager: 2.98 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: 0.04 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: 2.610 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- 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 : 0.003 0.051 9306 Z= 0.154 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS D 228 PHE 0.014 0.001 PHE D 65 TYR 0.024 0.001 TYR D 151 ARG 0.002 0.000 ARG D 442 *********************** 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 : 0.914 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: 0.2089 time to fit residues: 89.5068 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 : 0.894 ------------------------------------------------------------------------------- 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 94 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165676 restraints weight = 12137.529| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.48 r_work: 0.3879 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9306 Z= 0.210 Angle : 0.596 7.487 12696 Z= 0.308 Chirality : 0.040 0.170 1414 Planarity : 0.005 0.057 1544 Dihedral : 5.821 50.331 1245 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.54 % Allowed : 13.19 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1120 helix: 0.34 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 80 HIS 0.014 0.001 HIS A 598 PHE 0.036 0.002 PHE A 359 TYR 0.020 0.002 TYR A 152 ARG 0.006 0.001 ARG A 341 *********************** 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: 43 poor density : 182 time to evaluate : 0.878 Fit side-chains REVERT: A 122 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7545 (mp0) REVERT: A 133 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: A 189 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6623 (tptt) REVERT: A 303 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7747 (mmtt) REVERT: A 367 TYR cc_start: 0.7737 (t80) cc_final: 0.7421 (t80) REVERT: A 377 GLU cc_start: 0.7644 (mt-10) cc_final: 0.6818 (mm-30) REVERT: A 519 LEU cc_start: 0.8420 (mt) cc_final: 0.8188 (mt) REVERT: A 548 TYR cc_start: 0.7857 (t80) cc_final: 0.6916 (t80) REVERT: A 563 LEU cc_start: 0.7389 (mt) cc_final: 0.7141 (mt) REVERT: A 615 LEU cc_start: 0.8111 (tt) cc_final: 0.7831 (mt) REVERT: D 107 MET cc_start: 0.5740 (mpp) cc_final: 0.5340 (mmp) REVERT: D 122 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7541 (mp0) REVERT: D 133 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: D 303 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7723 (mmtt) REVERT: D 332 TYR cc_start: 0.7796 (m-80) cc_final: 0.7531 (m-80) REVERT: D 367 TYR cc_start: 0.7691 (t80) cc_final: 0.7366 (t80) REVERT: D 377 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6822 (mm-30) REVERT: D 519 LEU cc_start: 0.8543 (mt) cc_final: 0.8275 (mt) REVERT: D 548 TYR cc_start: 0.7822 (t80) cc_final: 0.6914 (t80) REVERT: D 563 LEU cc_start: 0.7442 (mt) cc_final: 0.7165 (mt) REVERT: D 615 LEU cc_start: 0.8120 (tt) cc_final: 0.7850 (mt) outliers start: 43 outliers final: 24 residues processed: 217 average time/residue: 0.1787 time to fit residues: 57.1417 Evaluate side-chains 192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.0170 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 228 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.187699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157858 restraints weight = 12284.093| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.53 r_work: 0.3797 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9306 Z= 0.189 Angle : 0.551 8.012 12696 Z= 0.282 Chirality : 0.039 0.181 1414 Planarity : 0.004 0.047 1544 Dihedral : 5.255 48.673 1234 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.38 % Allowed : 17.19 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1120 helix: 0.72 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 517 HIS 0.007 0.001 HIS D 598 PHE 0.015 0.001 PHE D 65 TYR 0.017 0.001 TYR A 151 ARG 0.004 0.000 ARG D 518 *********************** 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 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.994 Fit side-chains REVERT: A 88 LYS cc_start: 0.8572 (pttt) cc_final: 0.8337 (ptpt) REVERT: A 122 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7613 (mp0) REVERT: A 133 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: A 189 LYS cc_start: 0.7352 (ttpt) cc_final: 0.6606 (tptt) REVERT: A 303 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7695 (mmtt) REVERT: A 367 TYR cc_start: 0.7934 (t80) cc_final: 0.7566 (t80) REVERT: A 377 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6812 (mm-30) REVERT: A 473 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.4082 (t0) REVERT: A 563 LEU cc_start: 0.7585 (mt) cc_final: 0.7283 (mt) REVERT: A 615 LEU cc_start: 0.8086 (tt) cc_final: 0.7830 (mt) REVERT: D 88 LYS cc_start: 0.8590 (pttt) cc_final: 0.8364 (ptpt) REVERT: D 120 ASN cc_start: 0.8449 (m-40) cc_final: 0.7340 (m110) REVERT: D 122 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7604 (mp0) REVERT: D 133 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: D 303 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7675 (mmtt) REVERT: D 367 TYR cc_start: 0.7848 (t80) cc_final: 0.7490 (t80) REVERT: D 377 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6860 (mm-30) REVERT: D 434 ASP cc_start: 0.8076 (t0) cc_final: 0.7872 (t0) REVERT: D 563 LEU cc_start: 0.7598 (mt) cc_final: 0.7284 (mt) REVERT: D 584 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6912 (tt) REVERT: D 615 LEU cc_start: 0.8081 (tt) cc_final: 0.7840 (mt) outliers start: 32 outliers final: 22 residues processed: 192 average time/residue: 0.1870 time to fit residues: 52.1900 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 280 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 280 HIS D 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142381 restraints weight = 12230.254| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.54 r_work: 0.3614 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9306 Z= 0.250 Angle : 0.610 8.118 12696 Z= 0.313 Chirality : 0.041 0.206 1414 Planarity : 0.004 0.041 1544 Dihedral : 5.219 46.559 1234 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.22 % Allowed : 16.67 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1120 helix: 0.85 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 517 HIS 0.005 0.001 HIS A 222 PHE 0.017 0.002 PHE D 409 TYR 0.016 0.002 TYR D 572 ARG 0.005 0.001 ARG A 518 *********************** 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 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: A 189 LYS cc_start: 0.7370 (ttpt) cc_final: 0.6555 (tptt) REVERT: A 303 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7665 (mmtt) REVERT: A 367 TYR cc_start: 0.8027 (t80) cc_final: 0.7589 (t80) REVERT: A 377 GLU cc_start: 0.7939 (mt-10) cc_final: 0.6941 (mm-30) REVERT: A 473 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6113 (t0) REVERT: A 540 PHE cc_start: 0.8817 (t80) cc_final: 0.8585 (t80) REVERT: A 586 GLU cc_start: 0.7128 (tt0) cc_final: 0.6879 (tt0) REVERT: A 615 LEU cc_start: 0.8105 (tt) cc_final: 0.7834 (mt) REVERT: D 133 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: D 303 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7664 (mmtt) REVERT: D 367 TYR cc_start: 0.7964 (t80) cc_final: 0.7530 (t80) REVERT: D 377 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7002 (mm-30) REVERT: D 473 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5363 (t0) REVERT: D 519 LEU cc_start: 0.8724 (mt) cc_final: 0.8494 (mt) REVERT: D 584 LEU cc_start: 0.7515 (mm) cc_final: 0.6927 (tt) REVERT: D 586 GLU cc_start: 0.7057 (tt0) cc_final: 0.6824 (tt0) REVERT: D 615 LEU cc_start: 0.8122 (tt) cc_final: 0.7826 (mt) outliers start: 40 outliers final: 25 residues processed: 191 average time/residue: 0.1870 time to fit residues: 51.8227 Evaluate side-chains 177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 198 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.175137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142610 restraints weight = 12303.431| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.49 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: 0.7568 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9306 Z= 0.210 Angle : 0.571 8.371 12696 Z= 0.292 Chirality : 0.039 0.165 1414 Planarity : 0.004 0.037 1544 Dihedral : 5.179 47.672 1230 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.90 % Allowed : 17.41 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1120 helix: 0.89 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.004 0.001 HIS A 178 PHE 0.016 0.001 PHE D 65 TYR 0.018 0.001 TYR D 151 ARG 0.002 0.000 ARG D 341 *********************** 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 186 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7594 (mp0) REVERT: A 133 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: A 189 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6513 (tptt) REVERT: A 377 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7100 (mm-30) REVERT: A 473 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.5718 (t0) REVERT: A 519 LEU cc_start: 0.8696 (mt) cc_final: 0.8470 (mt) REVERT: A 540 PHE cc_start: 0.8907 (t80) cc_final: 0.8639 (t80) REVERT: A 597 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 615 LEU cc_start: 0.8102 (tt) cc_final: 0.7807 (mt) REVERT: D 122 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7593 (mp0) REVERT: D 133 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: D 303 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7682 (mmtt) REVERT: D 367 TYR cc_start: 0.8058 (t80) cc_final: 0.7628 (t80) REVERT: D 377 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7045 (mm-30) REVERT: D 519 LEU cc_start: 0.8716 (mt) cc_final: 0.8470 (mt) REVERT: D 584 LEU cc_start: 0.7509 (mm) cc_final: 0.6907 (tt) REVERT: D 615 LEU cc_start: 0.8152 (tt) cc_final: 0.7860 (mt) outliers start: 37 outliers final: 27 residues processed: 181 average time/residue: 0.1812 time to fit residues: 47.9433 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 87 optimal weight: 0.0060 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145436 restraints weight = 12256.629| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.48 r_work: 0.3663 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9306 Z= 0.176 Angle : 0.546 7.614 12696 Z= 0.279 Chirality : 0.038 0.155 1414 Planarity : 0.004 0.035 1544 Dihedral : 5.134 49.397 1230 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.69 % Allowed : 17.30 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1120 helix: 1.05 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 517 HIS 0.004 0.001 HIS D 178 PHE 0.015 0.001 PHE D 65 TYR 0.030 0.001 TYR D 151 ARG 0.002 0.000 ARG D 341 *********************** 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 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7579 (mp0) REVERT: A 133 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: A 189 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6451 (tptt) REVERT: A 303 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7715 (mmtt) REVERT: A 342 ASP cc_start: 0.8262 (t0) cc_final: 0.7938 (t0) REVERT: A 367 TYR cc_start: 0.7969 (t80) cc_final: 0.7573 (t80) REVERT: A 377 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7211 (mm-30) REVERT: A 473 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.5831 (t0) REVERT: A 597 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 615 LEU cc_start: 0.8112 (tt) cc_final: 0.7821 (mt) REVERT: D 122 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7601 (mp0) REVERT: D 133 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: D 303 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7697 (mmtt) REVERT: D 377 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7148 (mm-30) REVERT: D 473 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5072 (t0) REVERT: D 584 LEU cc_start: 0.7544 (mm) cc_final: 0.6952 (tt) REVERT: D 615 LEU cc_start: 0.8107 (tt) cc_final: 0.7829 (mt) outliers start: 35 outliers final: 21 residues processed: 174 average time/residue: 0.1944 time to fit residues: 48.8483 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 333 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136124 restraints weight = 12482.095| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.42 r_work: 0.3548 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9306 Z= 0.293 Angle : 0.620 9.368 12696 Z= 0.322 Chirality : 0.042 0.171 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.313 50.985 1230 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.22 % Allowed : 16.03 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1120 helix: 0.90 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 235 HIS 0.006 0.001 HIS A 178 PHE 0.018 0.002 PHE A 409 TYR 0.022 0.002 TYR A 572 ARG 0.003 0.000 ARG A 216 *********************** 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 174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.985 Fit side-chains REVERT: A 122 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7554 (mp0) REVERT: A 133 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: A 184 ASN cc_start: 0.6915 (m110) cc_final: 0.6596 (m110) REVERT: A 189 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6499 (tptt) REVERT: A 303 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7749 (mmtt) REVERT: A 367 TYR cc_start: 0.8146 (t80) cc_final: 0.7715 (t80) REVERT: A 377 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7115 (mm-30) REVERT: A 597 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 615 LEU cc_start: 0.8174 (tt) cc_final: 0.7861 (mt) REVERT: D 107 MET cc_start: 0.7136 (mmt) cc_final: 0.6863 (mmm) REVERT: D 122 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7579 (mp0) REVERT: D 133 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: D 184 ASN cc_start: 0.6953 (m110) cc_final: 0.6683 (m110) REVERT: D 367 TYR cc_start: 0.8112 (t80) cc_final: 0.7746 (t80) REVERT: D 377 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7198 (mm-30) REVERT: D 584 LEU cc_start: 0.7546 (mm) cc_final: 0.6948 (tt) REVERT: D 615 LEU cc_start: 0.8188 (tt) cc_final: 0.7878 (mt) outliers start: 40 outliers final: 30 residues processed: 165 average time/residue: 0.1839 time to fit residues: 45.1200 Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 535 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 137 VAL 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 268 THR 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 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 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 104 optimal weight: 0.0060 chunk 61 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 555 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 198 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140896 restraints weight = 12509.646| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.49 r_work: 0.3600 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9306 Z= 0.189 Angle : 0.562 8.943 12696 Z= 0.290 Chirality : 0.039 0.159 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.226 51.218 1228 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.38 % Allowed : 17.41 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1120 helix: 1.04 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.56 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS A 178 PHE 0.016 0.001 PHE D 65 TYR 0.031 0.001 TYR D 151 ARG 0.003 0.000 ARG D 216 *********************** 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 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.064 Fit side-chains REVERT: A 122 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7539 (mp0) REVERT: A 133 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: A 184 ASN cc_start: 0.6948 (m110) cc_final: 0.6648 (m110) REVERT: A 189 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6478 (tptt) REVERT: A 342 ASP cc_start: 0.8196 (t0) cc_final: 0.7856 (t0) REVERT: A 367 TYR cc_start: 0.8083 (t80) cc_final: 0.7673 (t80) REVERT: A 377 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7161 (mm-30) REVERT: A 471 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6843 (tp) REVERT: A 473 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.5817 (t0) REVERT: A 597 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 615 LEU cc_start: 0.8134 (tt) cc_final: 0.7839 (mt) REVERT: D 122 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7585 (mp0) REVERT: D 133 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: D 184 ASN cc_start: 0.7017 (m110) cc_final: 0.6789 (m110) REVERT: D 303 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7717 (mmtt) REVERT: D 342 ASP cc_start: 0.8175 (t0) cc_final: 0.7836 (t0) REVERT: D 367 TYR cc_start: 0.8090 (t80) cc_final: 0.7716 (t80) REVERT: D 377 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7192 (mm-30) REVERT: D 473 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.5663 (t0) REVERT: D 584 LEU cc_start: 0.7497 (mm) cc_final: 0.6910 (tt) REVERT: D 615 LEU cc_start: 0.8141 (tt) cc_final: 0.7844 (mt) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 0.1758 time to fit residues: 42.8360 Evaluate side-chains 163 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 535 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 473 ASP 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 103 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.171973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139285 restraints weight = 12391.482| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.48 r_work: 0.3582 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9306 Z= 0.217 Angle : 0.587 9.205 12696 Z= 0.303 Chirality : 0.040 0.193 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.242 52.526 1228 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.69 % Allowed : 17.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1120 helix: 1.00 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS D 178 PHE 0.016 0.001 PHE D 65 TYR 0.027 0.001 TYR D 151 ARG 0.003 0.000 ARG D 216 *********************** 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 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.916 Fit side-chains REVERT: A 133 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: A 184 ASN cc_start: 0.6923 (m110) cc_final: 0.6691 (m110) REVERT: A 189 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6497 (tptt) REVERT: A 342 ASP cc_start: 0.8216 (t0) cc_final: 0.7862 (t0) REVERT: A 367 TYR cc_start: 0.8182 (t80) cc_final: 0.7761 (t80) REVERT: A 377 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7237 (mm-30) REVERT: A 473 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6040 (t0) REVERT: A 597 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8319 (mt-10) REVERT: A 615 LEU cc_start: 0.8138 (tt) cc_final: 0.7832 (mt) REVERT: D 133 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: D 303 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7720 (mmtt) REVERT: D 342 ASP cc_start: 0.8199 (t0) cc_final: 0.7863 (t0) REVERT: D 367 TYR cc_start: 0.8104 (t80) cc_final: 0.7711 (t80) REVERT: D 377 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7239 (mm-30) REVERT: D 424 MET cc_start: 0.8360 (mmm) cc_final: 0.8009 (mtt) REVERT: D 584 LEU cc_start: 0.7476 (mm) cc_final: 0.6891 (tt) REVERT: D 615 LEU cc_start: 0.8145 (tt) cc_final: 0.7848 (mt) outliers start: 35 outliers final: 29 residues processed: 164 average time/residue: 0.1787 time to fit residues: 43.2815 Evaluate side-chains 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 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 538 ILE 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 82 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4060 r_free = 0.4060 target = 0.172417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139170 restraints weight = 12443.095| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.49 r_work: 0.3577 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9306 Z= 0.208 Angle : 0.588 9.116 12696 Z= 0.303 Chirality : 0.040 0.196 1414 Planarity : 0.004 0.035 1544 Dihedral : 5.217 52.039 1228 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.80 % Allowed : 18.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1120 helix: 1.03 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.64 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.004 0.001 HIS A 220 PHE 0.047 0.001 PHE A 213 TYR 0.028 0.001 TYR D 151 ARG 0.003 0.000 ARG A 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.912 Fit side-chains REVERT: A 122 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7519 (mp0) REVERT: A 133 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: A 189 LYS cc_start: 0.7330 (ttpt) cc_final: 0.6525 (tptt) REVERT: A 342 ASP cc_start: 0.8195 (t0) cc_final: 0.7835 (t0) REVERT: A 367 TYR cc_start: 0.8185 (t80) cc_final: 0.7766 (t80) REVERT: A 377 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7199 (mm-30) REVERT: A 473 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.5904 (t0) REVERT: A 597 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 615 LEU cc_start: 0.8131 (tt) cc_final: 0.7827 (mt) REVERT: D 122 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7537 (mp0) REVERT: D 133 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: D 184 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.5970 (p0) REVERT: D 342 ASP cc_start: 0.8194 (t0) cc_final: 0.7818 (t0) REVERT: D 367 TYR cc_start: 0.8155 (t80) cc_final: 0.7763 (t80) REVERT: D 377 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7223 (mm-30) REVERT: D 424 MET cc_start: 0.8288 (mmm) cc_final: 0.7980 (mtt) REVERT: D 473 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.5741 (t0) REVERT: D 584 LEU cc_start: 0.7449 (mm) cc_final: 0.6870 (tt) REVERT: D 615 LEU cc_start: 0.8119 (tt) cc_final: 0.7823 (mt) outliers start: 36 outliers final: 29 residues processed: 161 average time/residue: 0.1681 time to fit residues: 40.2444 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 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 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 538 ILE 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 75 optimal weight: 0.0030 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 105 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.2258 ------------------------------------------------------------------------------- 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 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.176099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143683 restraints weight = 12257.091| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.48 r_work: 0.3633 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9306 Z= 0.168 Angle : 0.568 8.759 12696 Z= 0.291 Chirality : 0.039 0.203 1414 Planarity : 0.004 0.036 1544 Dihedral : 5.170 52.114 1228 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.27 % Allowed : 19.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1120 helix: 1.11 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.56 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.003 0.001 HIS A 598 PHE 0.049 0.001 PHE A 213 TYR 0.032 0.001 TYR D 151 ARG 0.002 0.000 ARG A 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.45 seconds wall clock time: 69 minutes 46.80 seconds (4186.80 seconds total)