Starting phenix.real_space_refine on Sat Aug 3 21:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_39070.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_39070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_39070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_39070.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y95_39070/08_2024/8y95_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 Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 607": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.46, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.73 Conformation dependent library (CDL) restraints added in 1.5 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: 0.95 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: 2.61 Time building geometry restraints manager: 4.02 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: 100.75 - 107.40: 301 107.40 - 114.05: 5161 114.05 - 120.70: 4186 120.70 - 127.35: 2908 127.35 - 134.00: 140 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: 0.00 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: 2.870 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 0.870 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: 0.2047 time to fit residues: 87.4706 Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 0.911 Fit side-chains REVERT: A 122 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7282 (mp0) REVERT: A 133 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: A 189 LYS cc_start: 0.6893 (ttpt) cc_final: 0.6655 (tptt) REVERT: A 303 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7771 (mmtt) REVERT: A 367 TYR cc_start: 0.7408 (t80) cc_final: 0.7183 (t80) REVERT: A 377 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6596 (mm-30) REVERT: A 519 LEU cc_start: 0.8301 (mt) cc_final: 0.8059 (mt) REVERT: A 548 TYR cc_start: 0.7776 (t80) cc_final: 0.7057 (t80) REVERT: A 563 LEU cc_start: 0.7286 (mt) cc_final: 0.7028 (mt) REVERT: A 615 LEU cc_start: 0.8157 (tt) cc_final: 0.7950 (mt) REVERT: D 107 MET cc_start: 0.5426 (mpp) cc_final: 0.5026 (mmp) REVERT: D 122 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7274 (mp0) REVERT: D 133 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: D 303 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7735 (mmtt) REVERT: D 367 TYR cc_start: 0.7333 (t80) cc_final: 0.7118 (t80) REVERT: D 377 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6656 (mm-30) REVERT: D 519 LEU cc_start: 0.8408 (mt) cc_final: 0.8131 (mt) REVERT: D 548 TYR cc_start: 0.7768 (t80) cc_final: 0.7097 (t80) REVERT: D 563 LEU cc_start: 0.7343 (mt) cc_final: 0.7060 (mt) REVERT: D 615 LEU cc_start: 0.8183 (tt) cc_final: 0.7981 (mt) outliers start: 43 outliers final: 24 residues processed: 217 average time/residue: 0.1723 time to fit residues: 54.8509 Evaluate side-chains 192 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 56 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9306 Z= 0.268 Angle : 0.626 9.182 12696 Z= 0.324 Chirality : 0.042 0.176 1414 Planarity : 0.004 0.046 1544 Dihedral : 5.352 48.310 1234 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.59 % Allowed : 17.19 % 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: 0.21 (0.25), residues: 1120 helix: 0.58 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 517 HIS 0.008 0.001 HIS A 598 PHE 0.018 0.002 PHE D 65 TYR 0.027 0.002 TYR D 572 ARG 0.004 0.001 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 200 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.007 Fit side-chains REVERT: A 133 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: A 189 LYS cc_start: 0.7102 (ttpt) cc_final: 0.6741 (tptt) REVERT: A 303 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7750 (mmtt) REVERT: A 367 TYR cc_start: 0.7658 (t80) cc_final: 0.7383 (t80) REVERT: A 377 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6812 (mm-30) REVERT: A 473 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.5134 (t0) REVERT: A 540 PHE cc_start: 0.8698 (t80) cc_final: 0.8472 (t80) REVERT: A 615 LEU cc_start: 0.8204 (tt) cc_final: 0.7971 (mt) REVERT: D 133 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: D 189 LYS cc_start: 0.7029 (ttpt) cc_final: 0.6777 (tptt) REVERT: D 303 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7743 (mmtt) REVERT: D 367 TYR cc_start: 0.7623 (t80) cc_final: 0.7340 (t80) REVERT: D 377 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6865 (mm-30) REVERT: D 584 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7266 (tt) REVERT: D 615 LEU cc_start: 0.8235 (tt) cc_final: 0.8010 (mt) outliers start: 34 outliers final: 22 residues processed: 193 average time/residue: 0.1749 time to fit residues: 49.3371 Evaluate side-chains 180 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL 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 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 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 579 SER 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 76 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 228 HIS ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4314 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= 0.212 Angle : 0.580 7.418 12696 Z= 0.296 Chirality : 0.039 0.168 1414 Planarity : 0.004 0.044 1544 Dihedral : 5.224 46.696 1234 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.69 % Allowed : 17.83 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.25), residues: 1120 helix: 0.83 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.64 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 517 HIS 0.004 0.001 HIS D 598 PHE 0.016 0.001 PHE D 65 TYR 0.029 0.001 TYR D 151 ARG 0.003 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 192 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7254 (mp0) REVERT: A 133 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: A 189 LYS cc_start: 0.7033 (ttpt) cc_final: 0.6643 (tptt) REVERT: A 303 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7728 (mmtt) REVERT: A 377 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6794 (mm-30) REVERT: A 473 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.5858 (t0) REVERT: A 615 LEU cc_start: 0.8193 (tt) cc_final: 0.7923 (mt) REVERT: D 122 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7257 (mp0) REVERT: D 133 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: D 189 LYS cc_start: 0.6988 (ttpt) cc_final: 0.6651 (tptt) REVERT: D 303 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7717 (mmtt) REVERT: D 367 TYR cc_start: 0.7605 (t80) cc_final: 0.7322 (t80) REVERT: D 377 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6894 (mm-30) REVERT: D 519 LEU cc_start: 0.8667 (mt) cc_final: 0.8406 (mt) REVERT: D 584 LEU cc_start: 0.7728 (mm) cc_final: 0.7208 (tt) REVERT: D 615 LEU cc_start: 0.8205 (tt) cc_final: 0.7941 (mt) outliers start: 35 outliers final: 22 residues processed: 187 average time/residue: 0.1884 time to fit residues: 51.1304 Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 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 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 280 HIS ** 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9306 Z= 0.195 Angle : 0.550 7.887 12696 Z= 0.283 Chirality : 0.039 0.163 1414 Planarity : 0.004 0.036 1544 Dihedral : 5.190 49.314 1230 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.11 % Allowed : 18.04 % 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: 0.62 (0.25), residues: 1120 helix: 0.94 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.57 (0.33), residues: 362 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 0.030 0.001 PHE A 540 TYR 0.027 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 fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7255 (mp0) REVERT: A 133 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: A 189 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6562 (tptt) REVERT: A 303 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7727 (mmtt) REVERT: A 367 TYR cc_start: 0.7633 (t80) cc_final: 0.7318 (t80) REVERT: A 377 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6913 (mm-30) REVERT: A 444 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 473 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.5056 (t0) REVERT: A 615 LEU cc_start: 0.8198 (tt) cc_final: 0.7944 (mt) REVERT: D 122 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7256 (mp0) REVERT: D 133 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: D 189 LYS cc_start: 0.6923 (ttpt) cc_final: 0.6522 (tptt) REVERT: D 303 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7717 (mmtt) REVERT: D 367 TYR cc_start: 0.7675 (t80) cc_final: 0.7347 (t80) REVERT: D 377 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6887 (mm-30) REVERT: D 473 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5414 (t0) REVERT: D 584 LEU cc_start: 0.7705 (mm) cc_final: 0.7196 (tt) REVERT: D 615 LEU cc_start: 0.8205 (tt) cc_final: 0.7956 (mt) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.1785 time to fit residues: 45.8061 Evaluate side-chains 171 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 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 A residue 588 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 280 HIS A 333 ASN A 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 280 HIS D 610 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9306 Z= 0.191 Angle : 0.548 7.841 12696 Z= 0.283 Chirality : 0.039 0.161 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.177 50.625 1230 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.11 % Allowed : 17.09 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.25), residues: 1120 helix: 1.05 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.64 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 517 HIS 0.004 0.001 HIS D 178 PHE 0.016 0.001 PHE A 65 TYR 0.025 0.001 TYR D 151 ARG 0.002 0.000 ARG A 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 181 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7241 (mp0) REVERT: A 133 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: A 189 LYS cc_start: 0.6913 (ttpt) cc_final: 0.6519 (tptt) REVERT: A 303 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7739 (mmtt) REVERT: A 367 TYR cc_start: 0.7664 (t80) cc_final: 0.7346 (t80) REVERT: A 377 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7040 (mm-30) REVERT: A 471 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6016 (tp) REVERT: A 473 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.5767 (t0) REVERT: A 615 LEU cc_start: 0.8162 (tt) cc_final: 0.7922 (mt) REVERT: D 122 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7238 (mp0) REVERT: D 133 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8588 (m-80) REVERT: D 189 LYS cc_start: 0.6919 (ttpt) cc_final: 0.6515 (tptt) REVERT: D 377 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6906 (mm-30) REVERT: D 473 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.4991 (t0) REVERT: D 584 LEU cc_start: 0.7720 (mm) cc_final: 0.7220 (tt) REVERT: D 615 LEU cc_start: 0.8169 (tt) cc_final: 0.7934 (mt) outliers start: 39 outliers final: 26 residues processed: 173 average time/residue: 0.1819 time to fit residues: 45.5122 Evaluate side-chains 171 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 444 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 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 579 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4780 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= 0.174 Angle : 0.536 7.918 12696 Z= 0.276 Chirality : 0.038 0.174 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.181 52.195 1230 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.22 % Allowed : 17.41 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.25), residues: 1120 helix: 1.15 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.004 0.001 HIS D 280 PHE 0.015 0.001 PHE D 65 TYR 0.026 0.001 TYR D 151 ARG 0.002 0.000 ARG A 341 *********************** 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 191 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: A 303 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7736 (mmtt) REVERT: A 342 ASP cc_start: 0.8159 (t0) cc_final: 0.7777 (t0) REVERT: A 367 TYR cc_start: 0.7736 (t80) cc_final: 0.7397 (t80) REVERT: A 377 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6996 (mm-30) REVERT: A 444 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 471 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6069 (tp) REVERT: A 473 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.4785 (t0) REVERT: A 615 LEU cc_start: 0.8145 (tt) cc_final: 0.7912 (mt) REVERT: D 133 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: D 184 ASN cc_start: 0.6509 (m-40) cc_final: 0.6279 (m110) REVERT: D 303 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7743 (mmtt) REVERT: D 342 ASP cc_start: 0.8082 (t0) cc_final: 0.7723 (t0) REVERT: D 367 TYR cc_start: 0.7640 (t80) cc_final: 0.7338 (t80) REVERT: D 377 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6862 (mm-30) REVERT: D 473 ASP cc_start: 0.6057 (OUTLIER) cc_final: 0.4929 (t0) REVERT: D 584 LEU cc_start: 0.7704 (mm) cc_final: 0.7192 (tt) REVERT: D 615 LEU cc_start: 0.8158 (tt) cc_final: 0.7931 (mt) outliers start: 40 outliers final: 29 residues processed: 181 average time/residue: 0.1819 time to fit residues: 47.7875 Evaluate side-chains 178 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 444 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 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 610 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9306 Z= 0.244 Angle : 0.583 8.732 12696 Z= 0.303 Chirality : 0.040 0.185 1414 Planarity : 0.004 0.033 1544 Dihedral : 5.258 52.291 1230 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.64 % Allowed : 17.51 % 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: 0.72 (0.25), residues: 1120 helix: 1.02 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.54 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 235 HIS 0.004 0.001 HIS D 178 PHE 0.016 0.001 PHE D 65 TYR 0.019 0.001 TYR D 151 ARG 0.005 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 184 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7168 (mp0) REVERT: A 133 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: A 303 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7759 (mmtt) REVERT: A 342 ASP cc_start: 0.8188 (t0) cc_final: 0.7794 (t0) REVERT: A 367 TYR cc_start: 0.7810 (t80) cc_final: 0.7457 (t80) REVERT: A 377 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6999 (mm-30) REVERT: A 473 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.5772 (t0) REVERT: A 597 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 615 LEU cc_start: 0.8222 (tt) cc_final: 0.7966 (mt) REVERT: D 122 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7220 (mp0) REVERT: D 133 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: D 303 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7767 (mmtt) REVERT: D 367 TYR cc_start: 0.7794 (t80) cc_final: 0.7465 (t80) REVERT: D 377 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7082 (mm-30) REVERT: D 584 LEU cc_start: 0.7753 (mm) cc_final: 0.7242 (tt) REVERT: D 615 LEU cc_start: 0.8238 (tt) cc_final: 0.7980 (mt) outliers start: 44 outliers final: 34 residues processed: 173 average time/residue: 0.1814 time to fit residues: 45.2838 Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 444 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU 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 228 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 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 509 MET Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 538 ILE 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 94 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 555 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9306 Z= 0.185 Angle : 0.564 8.924 12696 Z= 0.289 Chirality : 0.039 0.175 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.210 50.841 1230 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.22 % Allowed : 17.83 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.25), residues: 1120 helix: 1.10 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.60 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 235 HIS 0.003 0.001 HIS A 178 PHE 0.015 0.001 PHE D 65 TYR 0.031 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 189 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7196 (mp0) REVERT: A 133 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: A 234 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6916 (mm-40) REVERT: A 303 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7752 (mmtt) REVERT: A 329 PHE cc_start: 0.7286 (m-10) cc_final: 0.7071 (m-10) REVERT: A 342 ASP cc_start: 0.8118 (t0) cc_final: 0.7722 (t0) REVERT: A 367 TYR cc_start: 0.7787 (t80) cc_final: 0.7450 (t80) REVERT: A 377 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7054 (mm-30) REVERT: A 473 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.4792 (t0) REVERT: A 597 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 615 LEU cc_start: 0.8198 (tt) cc_final: 0.7951 (mt) REVERT: D 113 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 122 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7221 (mp0) REVERT: D 133 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: D 303 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7763 (mmtt) REVERT: D 342 ASP cc_start: 0.8067 (t0) cc_final: 0.7695 (t0) REVERT: D 367 TYR cc_start: 0.7723 (t80) cc_final: 0.7409 (t80) REVERT: D 377 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7081 (mm-30) REVERT: D 473 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.5634 (t0) REVERT: D 584 LEU cc_start: 0.7711 (mm) cc_final: 0.7206 (tt) REVERT: D 615 LEU cc_start: 0.8177 (tt) cc_final: 0.7945 (mt) outliers start: 40 outliers final: 31 residues processed: 178 average time/residue: 0.1801 time to fit residues: 47.0909 Evaluate side-chains 177 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 444 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 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain 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 349 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9306 Z= 0.235 Angle : 0.608 9.312 12696 Z= 0.313 Chirality : 0.041 0.201 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.252 51.596 1230 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.11 % Allowed : 18.35 % Favored : 77.53 % 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 : -0.55 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.004 0.001 HIS A 178 PHE 0.016 0.001 PHE D 65 TYR 0.021 0.001 TYR D 151 ARG 0.002 0.000 ARG D 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 178 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7218 (mp0) REVERT: A 133 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: A 155 ILE cc_start: 0.7023 (tt) cc_final: 0.6782 (mt) REVERT: A 303 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7761 (mmtt) REVERT: A 342 ASP cc_start: 0.8175 (t0) cc_final: 0.7779 (t0) REVERT: A 367 TYR cc_start: 0.7841 (t80) cc_final: 0.7501 (t80) REVERT: A 377 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7134 (mm-30) REVERT: A 473 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.5499 (t0) REVERT: A 597 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8148 (mt-10) REVERT: A 615 LEU cc_start: 0.8220 (tt) cc_final: 0.7962 (mt) REVERT: D 122 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7215 (mp0) REVERT: D 133 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: D 303 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7769 (mmtt) REVERT: D 329 PHE cc_start: 0.7357 (m-10) cc_final: 0.7097 (m-10) REVERT: D 342 ASP cc_start: 0.8105 (t0) cc_final: 0.7722 (t0) REVERT: D 367 TYR cc_start: 0.7799 (t80) cc_final: 0.7468 (t80) REVERT: D 377 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7149 (mm-30) REVERT: D 584 LEU cc_start: 0.7711 (mm) cc_final: 0.7204 (tt) REVERT: D 615 LEU cc_start: 0.8221 (tt) cc_final: 0.7970 (mt) outliers start: 39 outliers final: 34 residues processed: 167 average time/residue: 0.1751 time to fit residues: 42.7703 Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 444 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 479 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 588 LEU 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 349 ILE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 534 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 27 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4063 r_free = 0.4063 target = 0.172646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139534 restraints weight = 12272.372| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.51 r_work: 0.3582 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5224 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= 0.199 Angle : 0.589 9.001 12696 Z= 0.302 Chirality : 0.040 0.181 1414 Planarity : 0.004 0.034 1544 Dihedral : 5.225 51.132 1230 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.90 % Allowed : 18.78 % Favored : 77.32 % 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: 0.82 (0.25), residues: 1120 helix: 1.09 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.51 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 235 HIS 0.003 0.001 HIS A 178 PHE 0.016 0.001 PHE D 65 TYR 0.022 0.001 TYR D 151 ARG 0.002 0.000 ARG D 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.63 seconds wall clock time: 38 minutes 20.10 seconds (2300.10 seconds total)