Starting phenix.real_space_refine on Wed Apr 10 00:26:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/04_2024/8qa6_18300_trim_updated.pdb" } resolution = 2.91 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= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 5826 2.51 5 N 1518 2.21 5 O 1696 1.98 5 H 8720 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B GLU 458": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Time building chain proxies: 8.47, per 1000 atoms: 0.48 Number of scatterers: 17808 At special positions: 0 Unit cell: (106.19, 116.522, 78.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 4 15.00 O 1696 8.00 N 1518 7.00 C 5826 6.00 H 8720 1.00 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: 13.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 43.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.971A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.834A pdb=" N LYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.676A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.767A pdb=" N LYS A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.531A pdb=" N PHE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 70 through 86 removed outlier: 3.970A pdb=" N ALA B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.822A pdb=" N LYS B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 291 through 310 Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.720A pdb=" N LEU B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.762A pdb=" N LYS B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 594 removed outlier: 3.534A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 632 through 643 Processing sheet with id= A, first strand: chain 'A' and resid 152 through 155 removed outlier: 4.125A pdb=" N ASN A 152 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 91 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N HIS A 127 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 93 " --> pdb=" O HIS A 127 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASP A 92 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 62 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR A 94 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 64 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 252 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS A 319 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR A 321 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 256 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 194 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR A 573 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 547 through 549 removed outlier: 6.488A pdb=" N PHE A 516 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR A 481 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 152 through 155 removed outlier: 4.123A pdb=" N ASN B 152 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 91 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N HIS B 127 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL B 93 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP B 92 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 62 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR B 94 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE B 64 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE B 252 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS B 319 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR B 321 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE B 256 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 194 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR B 573 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 547 through 549 removed outlier: 6.483A pdb=" N PHE B 516 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1023 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: 6.85 Time building geometry restraints manager: 14.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8702 1.03 - 1.22: 18 1.22 - 1.42: 3990 1.42 - 1.62: 5266 1.62 - 1.81: 80 Bond restraints: 18056 Sorted by residual: bond pdb=" C2' SAM B 701 " pdb=" C3' SAM B 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM A 701 " pdb=" C3' SAM A 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM B 703 " pdb=" C3' SAM B 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C2' SAM A 703 " pdb=" C3' SAM A 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C6 SAM A 703 " pdb=" N6 SAM A 703 " ideal model delta sigma weight residual 1.333 1.456 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 18051 not shown) Histogram of bond angle deviations from ideal: 96.41 - 108.47: 5726 108.47 - 120.53: 21889 120.53 - 132.59: 4939 132.59 - 144.65: 30 144.65 - 156.71: 4 Bond angle restraints: 32588 Sorted by residual: angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C8 SAM B 703 " ideal model delta sigma weight residual 123.85 96.41 27.44 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C8 SAM A 703 " ideal model delta sigma weight residual 123.85 96.45 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C4 SAM B 703 " ideal model delta sigma weight residual 130.15 156.71 -26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C4 SAM A 703 " ideal model delta sigma weight residual 130.15 156.60 -26.45 3.00e+00 1.11e-01 7.78e+01 angle pdb=" C1' SAM B 701 " pdb=" N9 SAM B 701 " pdb=" C8 SAM B 701 " ideal model delta sigma weight residual 123.85 98.83 25.02 3.00e+00 1.11e-01 6.96e+01 ... (remaining 32583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 8233 34.91 - 69.81: 373 69.81 - 104.72: 34 104.72 - 139.62: 0 139.62 - 174.53: 2 Dihedral angle restraints: 8642 sinusoidal: 4752 harmonic: 3890 Sorted by residual: dihedral pdb=" O5' FAD A 702 " pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.76 -174.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' FAD B 702 " pdb=" O3P FAD B 702 " pdb=" P FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.71 -174.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA ILE B 192 " pdb=" C ILE B 192 " pdb=" N CYS B 193 " pdb=" CA CYS B 193 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1360 0.323 - 0.646: 4 0.646 - 0.969: 0 0.969 - 1.292: 0 1.292 - 1.616: 4 Chirality restraints: 1368 Sorted by residual: chirality pdb=" SD SAM B 701 " pdb=" CG SAM B 701 " pdb=" CE SAM B 701 " pdb=" C5' SAM B 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" SD SAM A 701 " pdb=" CG SAM A 701 " pdb=" CE SAM A 701 " pdb=" C5' SAM A 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" SD SAM A 703 " pdb=" CG SAM A 703 " pdb=" CE SAM A 703 " pdb=" C5' SAM A 703 " both_signs ideal model delta sigma weight residual False 5.50 3.94 1.57 2.00e-01 2.50e+01 6.14e+01 ... (remaining 1365 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 152 " 0.056 2.00e-02 2.50e+03 6.90e-02 7.14e+01 pdb=" CG ASN B 152 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 152 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 152 " -0.108 2.00e-02 2.50e+03 pdb="HD21 ASN B 152 " -0.006 2.00e-02 2.50e+03 pdb="HD22 ASN B 152 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 152 " -0.055 2.00e-02 2.50e+03 6.87e-02 7.08e+01 pdb=" CG ASN A 152 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 152 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 152 " 0.108 2.00e-02 2.50e+03 pdb="HD21 ASN A 152 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN A 152 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 118 " -0.038 2.00e-02 2.50e+03 4.61e-02 3.19e+01 pdb=" CG ASN A 118 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 118 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 118 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 118 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 118 " -0.071 2.00e-02 2.50e+03 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 929 2.17 - 2.78: 34707 2.78 - 3.39: 51438 3.39 - 3.99: 66458 3.99 - 4.60: 103306 Nonbonded interactions: 256838 Sorted by model distance: nonbonded pdb=" OE1 GLU A 568 " pdb="HE22 GLN B 571 " model vdw 1.565 1.850 nonbonded pdb="HE22 GLN A 571 " pdb=" OE1 GLU B 568 " model vdw 1.566 1.850 nonbonded pdb="HE21 GLN A 555 " pdb=" H GLU B 568 " model vdw 1.605 2.100 nonbonded pdb=" HZ3 LYS B 584 " pdb=" OD1 ASP B 585 " model vdw 1.669 1.850 nonbonded pdb=" O VAL B 240 " pdb=" HG1 THR B 244 " model vdw 1.670 1.850 ... (remaining 256833 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=0.00 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: 2.980 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: 0.260 Extract box with map and model: 14.370 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 60.380 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.010 0.285 9336 Z= 0.668 Angle : 1.084 27.438 12696 Z= 0.428 Chirality : 0.098 1.616 1368 Planarity : 0.006 0.094 1608 Dihedral : 17.507 174.526 3576 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.52 % Allowed : 18.92 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1094 helix: -0.01 (0.23), residues: 470 sheet: -0.08 (0.37), residues: 176 loop : -0.69 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 95 HIS 0.006 0.001 HIS B 181 PHE 0.021 0.001 PHE A 582 TYR 0.017 0.002 TYR B 90 ARG 0.009 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7861 (mmt) cc_final: 0.7466 (mmt) outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 1.9399 time to fit residues: 225.9889 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain B residue 119 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9336 Z= 0.333 Angle : 0.620 6.944 12696 Z= 0.311 Chirality : 0.043 0.150 1368 Planarity : 0.005 0.045 1608 Dihedral : 11.209 164.526 1418 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.91 % Allowed : 17.15 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1094 helix: 1.27 (0.24), residues: 472 sheet: 0.18 (0.39), residues: 178 loop : -0.14 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 95 HIS 0.005 0.001 HIS B 539 PHE 0.026 0.002 PHE B 582 TYR 0.013 0.002 TYR B 512 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7350 (mp0) REVERT: A 445 ARG cc_start: 0.7293 (ptp90) cc_final: 0.7085 (ptp90) REVERT: A 473 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6746 (tmm160) REVERT: B 137 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6451 (mm-30) REVERT: B 399 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7358 (mp0) REVERT: B 445 ARG cc_start: 0.7291 (ptp90) cc_final: 0.7081 (ptp90) outliers start: 28 outliers final: 12 residues processed: 126 average time/residue: 2.2197 time to fit residues: 304.5209 Evaluate side-chains 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 634 GLN B 477 GLN B 634 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9336 Z= 0.251 Angle : 0.549 4.406 12696 Z= 0.276 Chirality : 0.041 0.144 1368 Planarity : 0.004 0.040 1608 Dihedral : 10.774 159.170 1414 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.77 % Allowed : 18.50 % Favored : 79.73 % 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: 1.13 (0.26), residues: 1094 helix: 1.66 (0.24), residues: 472 sheet: 0.34 (0.39), residues: 178 loop : 0.04 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.020 0.002 PHE A 582 TYR 0.011 0.001 TYR B 512 ARG 0.005 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7355 (mp0) REVERT: B 399 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7356 (mp0) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 2.1093 time to fit residues: 278.3124 Evaluate side-chains 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9336 Z= 0.211 Angle : 0.526 4.376 12696 Z= 0.264 Chirality : 0.040 0.141 1368 Planarity : 0.004 0.040 1608 Dihedral : 10.575 159.987 1414 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 18.19 % Favored : 79.94 % 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: 1.38 (0.26), residues: 1094 helix: 1.87 (0.24), residues: 472 sheet: 0.42 (0.39), residues: 180 loop : 0.18 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.018 0.002 PHE A 582 TYR 0.011 0.001 TYR B 512 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7349 (mp0) REVERT: A 460 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 473 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7310 (tmm160) REVERT: A 594 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8295 (mm110) REVERT: B 399 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7353 (mp0) REVERT: B 460 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 473 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6573 (tmm160) REVERT: B 594 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8305 (mm110) outliers start: 18 outliers final: 12 residues processed: 126 average time/residue: 2.2481 time to fit residues: 307.1983 Evaluate side-chains 125 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 555 GLN B 485 GLN B 555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9336 Z= 0.137 Angle : 0.481 4.189 12696 Z= 0.239 Chirality : 0.039 0.138 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.228 164.956 1414 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.29 % Allowed : 17.98 % Favored : 79.73 % 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 (0.27), residues: 1094 helix: 2.19 (0.24), residues: 472 sheet: 0.56 (0.39), residues: 180 loop : 0.34 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 95 HIS 0.004 0.001 HIS B 181 PHE 0.014 0.001 PHE A 582 TYR 0.010 0.001 TYR B 512 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7367 (mp0) REVERT: A 473 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7314 (tmm160) REVERT: A 594 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8295 (mm110) REVERT: B 473 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6646 (tmm160) REVERT: B 594 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8294 (mm110) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 2.0542 time to fit residues: 287.0082 Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9336 Z= 0.257 Angle : 0.534 4.439 12696 Z= 0.268 Chirality : 0.041 0.136 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.612 157.489 1414 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 18.92 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1094 helix: 2.21 (0.24), residues: 462 sheet: 0.51 (0.39), residues: 180 loop : 0.09 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.003 0.001 HIS B 181 PHE 0.017 0.002 PHE A 582 TYR 0.013 0.002 TYR A 512 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 473 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7374 (tmm160) REVERT: A 555 GLN cc_start: 0.8531 (tp40) cc_final: 0.7843 (tp-100) REVERT: A 594 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8298 (mm110) REVERT: B 399 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7387 (mp0) REVERT: B 473 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6699 (tmm160) REVERT: B 594 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8310 (mm110) outliers start: 19 outliers final: 12 residues processed: 125 average time/residue: 2.1916 time to fit residues: 297.6868 Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9336 Z= 0.196 Angle : 0.505 4.314 12696 Z= 0.252 Chirality : 0.039 0.136 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.473 159.933 1414 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.29 % Allowed : 19.33 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1094 helix: 2.38 (0.24), residues: 460 sheet: 0.46 (0.40), residues: 172 loop : 0.25 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.003 0.001 HIS B 181 PHE 0.016 0.001 PHE B 582 TYR 0.010 0.001 TYR A 512 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7395 (mp0) REVERT: A 419 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7532 (tptp) REVERT: A 473 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7378 (tmm160) REVERT: A 555 GLN cc_start: 0.8436 (tp40) cc_final: 0.8225 (tp-100) REVERT: B 399 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7380 (mp0) REVERT: B 419 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7536 (tptp) REVERT: B 473 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6714 (tmm160) REVERT: B 594 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8358 (mm110) outliers start: 22 outliers final: 11 residues processed: 123 average time/residue: 2.1629 time to fit residues: 290.5146 Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9336 Z= 0.161 Angle : 0.488 4.406 12696 Z= 0.242 Chirality : 0.039 0.135 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.335 161.979 1414 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 19.75 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1094 helix: 2.34 (0.24), residues: 472 sheet: 0.50 (0.40), residues: 172 loop : 0.52 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 95 HIS 0.003 0.001 HIS B 181 PHE 0.015 0.001 PHE B 582 TYR 0.009 0.001 TYR B 512 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7406 (mp0) REVERT: A 419 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7524 (tptp) REVERT: A 473 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7381 (tmm160) REVERT: A 555 GLN cc_start: 0.8457 (tp40) cc_final: 0.7945 (tp-100) REVERT: B 399 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7380 (mp0) REVERT: B 419 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7523 (tptp) REVERT: B 473 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6716 (tmm160) REVERT: B 594 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8346 (mm110) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 2.1341 time to fit residues: 286.1022 Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9336 Z= 0.160 Angle : 0.483 4.384 12696 Z= 0.240 Chirality : 0.039 0.135 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.276 162.780 1414 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.98 % Allowed : 19.85 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.27), residues: 1094 helix: 2.45 (0.24), residues: 470 sheet: 0.57 (0.40), residues: 180 loop : 0.53 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.014 0.001 PHE B 582 TYR 0.010 0.001 TYR A 512 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 419 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7522 (tptp) REVERT: A 473 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7364 (tmm160) REVERT: A 555 GLN cc_start: 0.8419 (tp40) cc_final: 0.7831 (mm-40) REVERT: B 399 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7382 (mp0) REVERT: B 419 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7517 (tptp) REVERT: B 473 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7029 (tmm160) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 2.1885 time to fit residues: 296.9978 Evaluate side-chains 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9336 Z= 0.138 Angle : 0.478 4.392 12696 Z= 0.237 Chirality : 0.038 0.136 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.204 164.362 1414 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.35 % Allowed : 20.48 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.27), residues: 1094 helix: 2.56 (0.24), residues: 466 sheet: 0.63 (0.40), residues: 180 loop : 0.57 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.013 0.001 PHE A 582 TYR 0.008 0.001 TYR B 512 ARG 0.007 0.000 ARG A 519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 419 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7508 (tptp) REVERT: A 473 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7371 (tmm160) REVERT: A 555 GLN cc_start: 0.8307 (tp40) cc_final: 0.8088 (tp-100) REVERT: B 399 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7387 (mp0) REVERT: B 419 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7509 (tptp) REVERT: B 473 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7041 (tmm160) outliers start: 13 outliers final: 10 residues processed: 120 average time/residue: 2.2216 time to fit residues: 289.9498 Evaluate side-chains 125 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123720 restraints weight = 31971.185| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.18 r_work: 0.3330 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9336 Z= 0.192 Angle : 0.497 5.058 12696 Z= 0.247 Chirality : 0.039 0.135 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.343 161.048 1414 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.25 % Allowed : 20.48 % Favored : 78.27 % 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: 2.09 (0.27), residues: 1094 helix: 2.54 (0.24), residues: 466 sheet: 0.53 (0.40), residues: 172 loop : 0.62 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.015 0.001 PHE B 582 TYR 0.011 0.001 TYR B 512 ARG 0.006 0.000 ARG A 519 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6713.95 seconds wall clock time: 119 minutes 56.89 seconds (7196.89 seconds total)