Starting phenix.real_space_refine on Mon Dec 11 13:12:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/12_2023/8qa6_18300_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/12_2023/8qa6_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_18300/12_2023/8qa6_18300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/12_2023/8qa6_18300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/12_2023/8qa6_18300_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa6_18300/12_2023/8qa6_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-1.21rc1-5172/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: 7.97, per 1000 atoms: 0.45 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: 15.61 Conformation dependent library (CDL) restraints added in 1.9 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: 3.17 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: 6.36 Time building geometry restraints manager: 15.98 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: 8041 34.91 - 69.81: 311 69.81 - 104.72: 34 104.72 - 139.62: 0 139.62 - 174.53: 2 Dihedral angle restraints: 8388 sinusoidal: 4498 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 8385 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: 9.850 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: 0.000 Extract box with map and model: 14.360 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 61.860 Find NCS groups from input model: 0.670 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.020 ------------------------------------------------------------------------------- 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 : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 1.8722 time to fit residues: 218.3783 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4918 time to fit residues: 3.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9336 Z= 0.365 Angle : 0.638 6.561 12696 Z= 0.321 Chirality : 0.044 0.148 1368 Planarity : 0.005 0.044 1608 Dihedral : 11.364 163.676 1414 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 17.36 % Favored : 79.83 % 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: 0.66 (0.26), residues: 1094 helix: 1.23 (0.24), residues: 472 sheet: 0.15 (0.39), residues: 178 loop : -0.18 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 95 HIS 0.005 0.001 HIS A 539 PHE 0.027 0.002 PHE B 582 TYR 0.014 0.002 TYR A 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: 27 poor density : 107 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 125 average time/residue: 2.0839 time to fit residues: 283.2786 Evaluate side-chains 117 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.2586 time to fit residues: 4.1447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A 634 GLN B 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1378 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= 0.209 Angle : 0.529 4.396 12696 Z= 0.265 Chirality : 0.040 0.145 1368 Planarity : 0.004 0.040 1608 Dihedral : 10.678 161.874 1414 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.56 % Allowed : 18.71 % 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: 1.20 (0.26), residues: 1094 helix: 1.74 (0.24), residues: 470 sheet: 0.34 (0.39), residues: 178 loop : 0.08 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS B 181 PHE 0.019 0.002 PHE A 582 TYR 0.010 0.001 TYR A 197 ARG 0.005 0.000 ARG A 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: 15 poor density : 112 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 122 average time/residue: 1.9784 time to fit residues: 264.7632 Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 6 average time/residue: 0.2664 time to fit residues: 4.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN B 477 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1605 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= 0.198 Angle : 0.515 4.397 12696 Z= 0.258 Chirality : 0.040 0.140 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.525 161.456 1414 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 17.98 % 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: 1.46 (0.26), residues: 1094 helix: 1.92 (0.24), residues: 472 sheet: 0.48 (0.39), residues: 180 loop : 0.24 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.004 0.001 HIS B 181 PHE 0.017 0.001 PHE A 582 TYR 0.011 0.001 TYR B 512 ARG 0.003 0.000 ARG A 51 *********************** 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 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 2.0610 time to fit residues: 282.9434 Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 6 average time/residue: 0.2786 time to fit residues: 4.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9336 Z= 0.180 Angle : 0.501 4.290 12696 Z= 0.249 Chirality : 0.039 0.139 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.412 161.904 1414 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.39 % Allowed : 17.78 % Favored : 79.83 % 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: 1.65 (0.26), residues: 1094 helix: 2.11 (0.24), residues: 472 sheet: 0.62 (0.40), residues: 180 loop : 0.28 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.004 0.001 HIS A 181 PHE 0.016 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.002 0.000 ARG B 51 *********************** 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 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 130 average time/residue: 1.9897 time to fit residues: 282.7997 Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 6 average time/residue: 0.2618 time to fit residues: 4.2726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1956 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= 0.218 Angle : 0.513 4.218 12696 Z= 0.257 Chirality : 0.040 0.137 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.490 159.550 1414 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 18.30 % Favored : 79.42 % 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: 2.11 (0.24), residues: 474 sheet: 0.62 (0.40), residues: 172 loop : 0.44 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.003 0.001 HIS A 181 PHE 0.016 0.001 PHE A 582 TYR 0.013 0.001 TYR B 512 ARG 0.002 0.000 ARG B 51 *********************** 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 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 1.9685 time to fit residues: 271.3723 Evaluate side-chains 122 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 6 average time/residue: 0.2636 time to fit residues: 4.3120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9336 Z= 0.220 Angle : 0.513 4.912 12696 Z= 0.257 Chirality : 0.040 0.136 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.508 159.265 1414 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 19.33 % Favored : 78.79 % 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: 1.77 (0.26), residues: 1094 helix: 2.17 (0.24), residues: 474 sheet: 0.54 (0.40), residues: 172 loop : 0.47 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.003 0.001 HIS A 181 PHE 0.016 0.001 PHE A 582 TYR 0.013 0.001 TYR A 512 ARG 0.002 0.000 ARG A 51 *********************** 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 125 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 121 average time/residue: 1.9654 time to fit residues: 261.5281 Evaluate side-chains 122 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 4 average time/residue: 0.3153 time to fit residues: 3.7961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 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: 2.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9336 Z= 0.235 Angle : 0.523 4.393 12696 Z= 0.263 Chirality : 0.040 0.135 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.572 158.318 1414 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.18 % Allowed : 19.02 % Favored : 78.79 % 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: 1.87 (0.26), residues: 1094 helix: 2.23 (0.24), residues: 470 sheet: 0.50 (0.40), residues: 172 loop : 0.60 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.003 0.001 HIS A 181 PHE 0.017 0.002 PHE B 582 TYR 0.012 0.001 TYR A 512 ARG 0.002 0.000 ARG A 51 *********************** 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 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 2.0120 time to fit residues: 272.7110 Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 4 average time/residue: 0.2337 time to fit residues: 3.3383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.0030 chunk 104 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 overall best weight: 0.4668 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2280 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= 0.139 Angle : 0.493 5.021 12696 Z= 0.244 Chirality : 0.039 0.137 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.296 162.759 1414 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.66 % Allowed : 20.27 % Favored : 78.07 % 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: 2.07 (0.27), residues: 1094 helix: 2.46 (0.24), residues: 470 sheet: 0.78 (0.40), residues: 180 loop : 0.55 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.003 0.001 HIS A 181 PHE 0.013 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.009 0.000 ARG A 519 *********************** 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 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 129 average time/residue: 1.8571 time to fit residues: 263.6208 Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 2 average time/residue: 0.2668 time to fit residues: 2.6993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2352 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= 0.209 Angle : 0.515 4.654 12696 Z= 0.258 Chirality : 0.040 0.134 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.427 159.909 1414 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.94 % Allowed : 20.69 % 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: 2.06 (0.27), residues: 1094 helix: 2.41 (0.24), residues: 470 sheet: 0.74 (0.41), residues: 172 loop : 0.60 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.005 0.001 HIS B 181 PHE 0.015 0.001 PHE A 582 TYR 0.015 0.001 TYR A 512 ARG 0.005 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 121 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 10 residues processed: 120 average time/residue: 1.9915 time to fit residues: 263.2164 Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 2 average time/residue: 0.2718 time to fit residues: 2.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122822 restraints weight = 32233.367| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.11 r_work: 0.3336 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9336 Z= 0.225 Angle : 0.520 5.339 12696 Z= 0.261 Chirality : 0.040 0.133 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.519 158.895 1414 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.83 % Allowed : 20.69 % 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: 2.00 (0.27), residues: 1094 helix: 2.35 (0.24), residues: 470 sheet: 0.66 (0.41), residues: 172 loop : 0.60 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.005 0.001 HIS B 448 PHE 0.016 0.001 PHE A 582 TYR 0.014 0.001 TYR A 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: 6317.26 seconds wall clock time: 111 minutes 58.44 seconds (6718.44 seconds total)