Starting phenix.real_space_refine on Fri Mar 15 04:37:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gso_34237/03_2024/8gso_34237_neut.pdb" } resolution = 3.3 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= 0.031 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7060 2.51 5 N 1700 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B GLU 607": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10624 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Chain: "B" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Time building chain proxies: 6.11, per 1000 atoms: 0.58 Number of scatterers: 10624 At special positions: 0 Unit cell: (119.262, 112.59, 100.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1828 8.00 N 1700 7.00 C 7060 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=0, symmetry=0 Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 110 Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN A 136 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 389 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.628A pdb=" N GLN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 484 removed outlier: 4.020A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR A 693 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 110 Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN B 136 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN B 353 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 389 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 477 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1851 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: 3.13 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1544 1.27 - 1.40: 2908 1.40 - 1.54: 6299 1.54 - 1.68: 95 1.68 - 1.81: 60 Bond restraints: 10906 Sorted by residual: bond pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C THR B 496 " pdb=" O THR B 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" C THR A 496 " pdb=" O THR A 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" N THR B 389 " pdb=" CA THR B 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.51e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.22: 145 103.22 - 111.16: 4196 111.16 - 119.09: 4831 119.09 - 127.02: 5539 127.02 - 134.96: 113 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N LYS A 145 " pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.88 12.00 1.23e+00 6.61e-01 9.51e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4960 17.46 - 34.91: 716 34.91 - 52.37: 485 52.37 - 69.82: 251 69.82 - 87.28: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: dihedral pdb=" C ILE B 397 " pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" CB ILE B 397 " ideal model delta harmonic sigma weight residual -122.00 -136.17 14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C ILE B 379 " pdb=" N ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C ILE A 379 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " pdb=" CB ILE A 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.221: 324 0.221 - 0.332: 57 0.332 - 0.442: 26 0.442 - 0.553: 10 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" C PRO B 499 " pdb=" CB PRO B 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 108 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO B 108 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 20 1.93 - 2.68: 842 2.68 - 3.42: 15677 3.42 - 4.16: 27139 4.16 - 4.90: 46532 Nonbonded interactions: 90210 Sorted by model distance: nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.407 3.200 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.407 3.200 nonbonded pdb=" CE2 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.446 3.340 ... (remaining 90205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.360 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: 7.420 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 31.310 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 0.013 0.103 10906 Z= 0.822 Angle : 1.663 14.670 14824 Z= 1.143 Chirality : 0.112 0.553 1722 Planarity : 0.014 0.185 1808 Dihedral : 25.120 87.276 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 6.70 % Allowed : 17.05 % Favored : 76.26 % Rotamer: Outliers : 41.49 % Allowed : 12.07 % Favored : 46.44 % Cbeta Deviations : 1.42 % 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: -5.21 (0.18), residues: 1314 helix: -2.57 (0.13), residues: 864 sheet: -6.27 (0.42), residues: 24 loop : -4.97 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS B 617 PHE 0.030 0.002 PHE B 513 TYR 0.010 0.002 TYR B 555 ARG 0.002 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 478 poor density : 314 time to evaluate : 1.319 Fit side-chains REVERT: A 2 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4439 (tt0) REVERT: A 104 PRO cc_start: 0.6399 (OUTLIER) cc_final: 0.5087 (Cg_exo) REVERT: A 120 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5664 (mmmt) REVERT: A 169 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7412 (tttm) REVERT: A 204 ASP cc_start: -0.0318 (OUTLIER) cc_final: -0.0536 (t0) REVERT: A 223 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 337 THR cc_start: 0.7627 (m) cc_final: 0.7148 (p) REVERT: A 420 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 466 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 481 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 532 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 607 GLU cc_start: 0.7583 (tp30) cc_final: 0.7127 (mm-30) REVERT: A 619 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8112 (mmt90) REVERT: B 2 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4550 (tt0) REVERT: B 104 PRO cc_start: 0.6415 (OUTLIER) cc_final: 0.5093 (Cg_exo) REVERT: B 169 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7415 (tttm) REVERT: B 204 ASP cc_start: -0.0315 (OUTLIER) cc_final: -0.0536 (t0) REVERT: B 223 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 337 THR cc_start: 0.7632 (m) cc_final: 0.7150 (p) REVERT: B 420 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 466 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 532 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 607 GLU cc_start: 0.7579 (tp30) cc_final: 0.7124 (mm-30) REVERT: B 619 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8107 (mmt90) outliers start: 478 outliers final: 87 residues processed: 634 average time/residue: 0.2493 time to fit residues: 213.8473 Evaluate side-chains 299 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 192 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 499 PRO Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 71 GLN A 75 ASN A 136 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 596 ASN A 628 GLN B 40 ASN B 71 GLN B 75 ASN B 136 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 596 ASN B 628 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10906 Z= 0.308 Angle : 0.881 8.281 14824 Z= 0.461 Chirality : 0.050 0.252 1722 Planarity : 0.008 0.088 1808 Dihedral : 13.202 65.186 1635 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 1.37 % Allowed : 14.23 % Favored : 84.40 % Rotamer: Outliers : 11.55 % Allowed : 23.70 % Favored : 64.76 % 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: -3.05 (0.21), residues: 1314 helix: -0.66 (0.16), residues: 896 sheet: -6.35 (0.35), residues: 24 loop : -4.99 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 49 HIS 0.003 0.001 HIS A 329 PHE 0.022 0.002 PHE B 369 TYR 0.014 0.002 TYR B 665 ARG 0.006 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 199 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4748 (OUTLIER) cc_final: 0.4523 (tt0) REVERT: A 337 THR cc_start: 0.7678 (m) cc_final: 0.7117 (p) REVERT: A 420 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 624 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 337 THR cc_start: 0.7671 (m) cc_final: 0.7123 (p) REVERT: B 420 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 478 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8268 (t) REVERT: B 624 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8983 (tp) outliers start: 133 outliers final: 57 residues processed: 309 average time/residue: 0.1808 time to fit residues: 83.5490 Evaluate side-chains 218 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 155 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10906 Z= 0.316 Angle : 0.799 9.125 14824 Z= 0.412 Chirality : 0.047 0.169 1722 Planarity : 0.006 0.071 1808 Dihedral : 10.172 71.185 1510 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.23 % Favored : 85.24 % Rotamer: Outliers : 8.33 % Allowed : 27.26 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.72 (0.23), residues: 1314 helix: 0.27 (0.17), residues: 880 sheet: -4.60 (1.11), residues: 10 loop : -4.24 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 613 HIS 0.005 0.001 HIS A 447 PHE 0.024 0.002 PHE B 513 TYR 0.009 0.001 TYR B 164 ARG 0.005 0.001 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 179 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6836 (ptp-170) REVERT: A 478 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8435 (m) REVERT: A 647 ILE cc_start: 0.8004 (tp) cc_final: 0.7683 (tp) REVERT: B 318 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.6815 (ptp-170) REVERT: B 647 ILE cc_start: 0.8015 (tp) cc_final: 0.7699 (tp) outliers start: 96 outliers final: 62 residues processed: 257 average time/residue: 0.1741 time to fit residues: 68.2884 Evaluate side-chains 227 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 162 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 476 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10906 Z= 0.230 Angle : 0.717 8.901 14824 Z= 0.367 Chirality : 0.044 0.157 1722 Planarity : 0.006 0.063 1808 Dihedral : 9.274 76.658 1493 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.33 % Favored : 87.14 % Rotamer: Outliers : 8.07 % Allowed : 29.43 % Favored : 62.50 % 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: -1.18 (0.24), residues: 1314 helix: 0.61 (0.18), residues: 882 sheet: -4.09 (1.29), residues: 10 loop : -3.88 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 548 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE B 131 TYR 0.010 0.001 TYR B 572 ARG 0.008 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 186 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.7342 (tp) cc_final: 0.6991 (tp) REVERT: A 573 SER cc_start: 0.8422 (t) cc_final: 0.8015 (m) REVERT: A 611 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7812 (tpt-90) REVERT: B 573 SER cc_start: 0.8433 (t) cc_final: 0.8052 (m) REVERT: B 611 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7822 (tpt-90) outliers start: 93 outliers final: 54 residues processed: 257 average time/residue: 0.1759 time to fit residues: 68.2390 Evaluate side-chains 201 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10906 Z= 0.295 Angle : 0.746 9.555 14824 Z= 0.382 Chirality : 0.045 0.176 1722 Planarity : 0.006 0.060 1808 Dihedral : 8.114 79.777 1474 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.47 % Favored : 85.92 % Rotamer: Outliers : 7.47 % Allowed : 28.21 % Favored : 64.32 % 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: -1.02 (0.24), residues: 1314 helix: 0.75 (0.18), residues: 882 sheet: -3.92 (1.38), residues: 10 loop : -3.86 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.023 0.002 PHE A 513 TYR 0.011 0.001 TYR A 634 ARG 0.006 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 141 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7151 (ppp) cc_final: 0.6854 (ppp) REVERT: A 390 LEU cc_start: 0.7505 (tp) cc_final: 0.7027 (tp) REVERT: A 573 SER cc_start: 0.8420 (t) cc_final: 0.8001 (m) REVERT: A 611 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8060 (tpt-90) REVERT: B 332 MET cc_start: 0.7159 (ppp) cc_final: 0.6866 (ppp) REVERT: B 573 SER cc_start: 0.8403 (t) cc_final: 0.8007 (m) REVERT: B 611 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8076 (tpt-90) outliers start: 86 outliers final: 62 residues processed: 203 average time/residue: 0.2006 time to fit residues: 60.3745 Evaluate side-chains 199 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 135 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10906 Z= 0.231 Angle : 0.696 7.729 14824 Z= 0.358 Chirality : 0.044 0.201 1722 Planarity : 0.005 0.058 1808 Dihedral : 7.769 88.767 1462 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.79 % Favored : 86.68 % Rotamer: Outliers : 6.60 % Allowed : 28.47 % Favored : 64.93 % 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: -0.74 (0.24), residues: 1314 helix: 0.93 (0.18), residues: 882 sheet: -4.55 (0.85), residues: 20 loop : -3.58 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 548 HIS 0.003 0.001 HIS A 531 PHE 0.019 0.001 PHE A 513 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 161 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7176 (ppp) cc_final: 0.6830 (ppp) REVERT: A 390 LEU cc_start: 0.7430 (tp) cc_final: 0.6966 (tp) REVERT: A 573 SER cc_start: 0.8324 (t) cc_final: 0.8001 (m) REVERT: A 611 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7833 (tpt-90) REVERT: B 332 MET cc_start: 0.7185 (ppp) cc_final: 0.6823 (ppp) REVERT: B 573 SER cc_start: 0.8336 (t) cc_final: 0.8016 (m) REVERT: B 611 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7828 (tpt-90) outliers start: 76 outliers final: 54 residues processed: 212 average time/residue: 0.2196 time to fit residues: 66.0542 Evaluate side-chains 198 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10906 Z= 0.263 Angle : 0.708 8.789 14824 Z= 0.363 Chirality : 0.044 0.179 1722 Planarity : 0.005 0.059 1808 Dihedral : 6.892 59.987 1451 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.77 % Favored : 85.69 % Rotamer: Outliers : 6.34 % Allowed : 27.78 % Favored : 65.89 % 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: -0.59 (0.24), residues: 1314 helix: 1.03 (0.18), residues: 882 sheet: -4.51 (0.88), residues: 20 loop : -3.48 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 548 HIS 0.005 0.001 HIS A 531 PHE 0.023 0.001 PHE B 513 TYR 0.010 0.001 TYR B 634 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 146 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7206 (ppp) cc_final: 0.6909 (ppp) REVERT: A 390 LEU cc_start: 0.7509 (tp) cc_final: 0.7022 (tp) REVERT: A 573 SER cc_start: 0.8363 (t) cc_final: 0.7997 (m) REVERT: A 611 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8068 (tpt-90) REVERT: B 332 MET cc_start: 0.7265 (ppp) cc_final: 0.6955 (ppp) REVERT: B 335 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7078 (mmtp) REVERT: B 573 SER cc_start: 0.8380 (t) cc_final: 0.8010 (m) REVERT: B 611 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8030 (tpt-90) outliers start: 73 outliers final: 59 residues processed: 197 average time/residue: 0.2124 time to fit residues: 60.5545 Evaluate side-chains 198 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 136 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10906 Z= 0.263 Angle : 0.711 10.695 14824 Z= 0.363 Chirality : 0.045 0.249 1722 Planarity : 0.005 0.056 1808 Dihedral : 6.862 59.631 1451 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.01 % Favored : 86.45 % Rotamer: Outliers : 6.42 % Allowed : 27.95 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.25), residues: 1314 helix: 1.09 (0.18), residues: 882 sheet: -4.44 (0.94), residues: 20 loop : -3.43 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 548 HIS 0.005 0.001 HIS A 531 PHE 0.021 0.001 PHE A 513 TYR 0.009 0.001 TYR B 364 ARG 0.004 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 150 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7207 (ppp) cc_final: 0.6935 (ppp) REVERT: A 335 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7023 (mmtp) REVERT: A 573 SER cc_start: 0.8363 (t) cc_final: 0.7979 (m) REVERT: A 611 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8022 (tpt-90) REVERT: B 198 ASP cc_start: 0.3595 (t0) cc_final: 0.3286 (t0) REVERT: B 332 MET cc_start: 0.7213 (ppp) cc_final: 0.6952 (ppp) REVERT: B 334 ASP cc_start: 0.4904 (t0) cc_final: 0.4693 (t0) REVERT: B 573 SER cc_start: 0.8377 (t) cc_final: 0.7983 (m) REVERT: B 611 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7991 (tpt-90) outliers start: 74 outliers final: 59 residues processed: 200 average time/residue: 0.2114 time to fit residues: 62.2251 Evaluate side-chains 205 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 143 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10906 Z= 0.226 Angle : 0.699 10.090 14824 Z= 0.354 Chirality : 0.044 0.240 1722 Planarity : 0.005 0.052 1808 Dihedral : 6.685 57.938 1451 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.46 % Allowed : 13.55 % Favored : 86.00 % Rotamer: Outliers : 5.38 % Allowed : 29.25 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1314 helix: 1.19 (0.18), residues: 882 sheet: -4.39 (0.93), residues: 20 loop : -3.35 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.001 PHE A 513 TYR 0.008 0.001 TYR B 634 ARG 0.011 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7019 (mmtp) REVERT: A 390 LEU cc_start: 0.7417 (tp) cc_final: 0.6926 (tp) REVERT: A 573 SER cc_start: 0.8310 (t) cc_final: 0.7965 (m) REVERT: B 198 ASP cc_start: 0.3562 (t0) cc_final: 0.3294 (t0) REVERT: B 573 SER cc_start: 0.8305 (t) cc_final: 0.7952 (m) outliers start: 62 outliers final: 51 residues processed: 198 average time/residue: 0.2033 time to fit residues: 58.4628 Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10906 Z= 0.323 Angle : 0.766 9.759 14824 Z= 0.388 Chirality : 0.046 0.213 1722 Planarity : 0.006 0.049 1808 Dihedral : 6.283 59.911 1444 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.77 % Favored : 85.84 % Rotamer: Outliers : 5.03 % Allowed : 29.69 % Favored : 65.28 % 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: -0.45 (0.24), residues: 1314 helix: 1.11 (0.18), residues: 894 sheet: -4.51 (0.94), residues: 20 loop : -3.48 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 26 HIS 0.005 0.001 HIS B 531 PHE 0.026 0.002 PHE A 513 TYR 0.014 0.001 TYR B 364 ARG 0.009 0.001 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 144 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7158 (ppp) cc_final: 0.6746 (ppp) REVERT: A 335 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7050 (mmtp) REVERT: A 573 SER cc_start: 0.8439 (t) cc_final: 0.8009 (m) REVERT: B 198 ASP cc_start: 0.3687 (t0) cc_final: 0.3415 (t0) REVERT: B 332 MET cc_start: 0.7173 (ppp) cc_final: 0.6838 (ppp) REVERT: B 334 ASP cc_start: 0.5049 (t0) cc_final: 0.4690 (t0) REVERT: B 573 SER cc_start: 0.8460 (t) cc_final: 0.8008 (m) outliers start: 58 outliers final: 47 residues processed: 179 average time/residue: 0.2060 time to fit residues: 54.0826 Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116416 restraints weight = 13326.115| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.36 r_work: 0.3239 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10906 Z= 0.229 Angle : 0.718 9.725 14824 Z= 0.363 Chirality : 0.044 0.198 1722 Planarity : 0.005 0.046 1808 Dihedral : 6.173 57.210 1444 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.39 % Favored : 86.23 % Rotamer: Outliers : 4.08 % Allowed : 30.30 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.25), residues: 1314 helix: 1.13 (0.18), residues: 906 sheet: -4.47 (0.94), residues: 20 loop : -3.47 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 548 HIS 0.005 0.001 HIS A 531 PHE 0.017 0.001 PHE B 513 TYR 0.008 0.001 TYR B 634 ARG 0.009 0.001 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2610.37 seconds wall clock time: 47 minutes 42.10 seconds (2862.10 seconds total)