Starting phenix.real_space_refine on Tue Feb 13 13:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/02_2024/7wxh_32879.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4054 2.51 5 N 1172 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6494 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Time building chain proxies: 4.19, per 1000 atoms: 0.65 Number of scatterers: 6494 At special positions: 0 Unit cell: (98.58, 94.34, 62.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1238 8.00 N 1172 7.00 C 4054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 47.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.266A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.126A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.629A pdb=" N THR A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.792A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.586A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 4.266A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.127A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.629A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.792A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.586A pdb=" N ALA B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 744 through 750 removed outlier: 7.301A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A 456 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 440 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 445 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 771 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.479A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.447A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.625A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.272A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 744 through 750 removed outlier: 7.300A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR B 456 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 440 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 445 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 771 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 487 through 490 removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.447A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 629 through 630 removed outlier: 6.625A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.273A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 840 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: 1.76 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.46: 1115 1.46 - 1.57: 3173 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6594 Sorted by residual: bond pdb=" C LYS B 629 " pdb=" N ILE B 630 " ideal model delta sigma weight residual 1.330 1.311 0.020 1.42e-02 4.96e+03 1.91e+00 bond pdb=" C ARG A 411 " pdb=" N LEU A 412 " ideal model delta sigma weight residual 1.334 1.316 0.019 1.38e-02 5.25e+03 1.85e+00 bond pdb=" CG LEU B 389 " pdb=" CD1 LEU B 389 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CG LEU A 389 " pdb=" CD1 LEU A 389 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CA GLY A 764 " pdb=" C GLY A 764 " ideal model delta sigma weight residual 1.519 1.509 0.009 7.00e-03 2.04e+04 1.78e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.60: 182 106.60 - 113.54: 3898 113.54 - 120.48: 2420 120.48 - 127.42: 2362 127.42 - 134.36: 66 Bond angle restraints: 8928 Sorted by residual: angle pdb=" CA LEU A 389 " pdb=" CB LEU A 389 " pdb=" CG LEU A 389 " ideal model delta sigma weight residual 116.30 134.36 -18.06 3.50e+00 8.16e-02 2.66e+01 angle pdb=" CA LEU B 389 " pdb=" CB LEU B 389 " pdb=" CG LEU B 389 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" C LEU B 389 " pdb=" N ASP B 390 " pdb=" CA ASP B 390 " ideal model delta sigma weight residual 120.29 115.40 4.89 1.42e+00 4.96e-01 1.19e+01 angle pdb=" C LEU A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta sigma weight residual 120.29 115.43 4.86 1.42e+00 4.96e-01 1.17e+01 angle pdb=" CA GLU A 526 " pdb=" CB GLU A 526 " pdb=" CG GLU A 526 " ideal model delta sigma weight residual 114.10 107.76 6.34 2.00e+00 2.50e-01 1.00e+01 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 3517 14.78 - 29.57: 376 29.57 - 44.35: 111 44.35 - 59.13: 28 59.13 - 73.92: 4 Dihedral angle restraints: 4036 sinusoidal: 1572 harmonic: 2464 Sorted by residual: dihedral pdb=" CA GLN B 638 " pdb=" C GLN B 638 " pdb=" N GLN B 639 " pdb=" CA GLN B 639 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLN A 638 " pdb=" C GLN A 638 " pdb=" N GLN A 639 " pdb=" CA GLN A 639 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA THR A 524 " pdb=" C THR A 524 " pdb=" N ARG A 525 " pdb=" CA ARG A 525 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 564 0.028 - 0.057: 286 0.057 - 0.085: 136 0.085 - 0.113: 49 0.113 - 0.142: 11 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CB ILE B 560 " pdb=" CA ILE B 560 " pdb=" CG1 ILE B 560 " pdb=" CG2 ILE B 560 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CB ILE A 560 " pdb=" CA ILE A 560 " pdb=" CG1 ILE A 560 " pdb=" CG2 ILE A 560 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1043 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 526 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" CD GLU B 526 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU B 526 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 526 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 526 " 0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" CD GLU A 526 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 526 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 526 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 579 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" CG ASP A 579 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP A 579 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 579 " -0.008 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 185 2.63 - 3.20: 7118 3.20 - 3.77: 10311 3.77 - 4.33: 13524 4.33 - 4.90: 21586 Nonbonded interactions: 52724 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" OD1 ASP A 548 " model vdw 2.067 2.440 nonbonded pdb=" OG SER B 546 " pdb=" OD1 ASP B 548 " model vdw 2.068 2.440 nonbonded pdb=" O ASN B 672 " pdb=" OG1 THR B 676 " model vdw 2.103 2.440 nonbonded pdb=" O ASN A 672 " pdb=" OG1 THR A 676 " model vdw 2.103 2.440 nonbonded pdb=" O ARG B 356 " pdb=" OG SER B 359 " model vdw 2.105 2.440 ... (remaining 52719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.630 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.350 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.006 0.044 6594 Z= 0.412 Angle : 0.864 18.061 8928 Z= 0.489 Chirality : 0.042 0.142 1046 Planarity : 0.004 0.032 1170 Dihedral : 14.117 73.918 2440 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.45 % Favored : 88.32 % Rotamer: Outliers : 1.74 % Allowed : 8.41 % Favored : 89.86 % 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: -4.55 (0.24), residues: 856 helix: -2.05 (0.22), residues: 352 sheet: -3.02 (0.39), residues: 144 loop : -3.99 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 768 HIS 0.007 0.002 HIS B 565 PHE 0.015 0.003 PHE B 706 TYR 0.009 0.001 TYR B 654 ARG 0.005 0.001 ARG B 735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9250 (t80) cc_final: 0.8741 (t80) REVERT: A 452 LEU cc_start: 0.9225 (tp) cc_final: 0.8886 (tt) REVERT: A 481 MET cc_start: 0.8116 (mtp) cc_final: 0.7595 (mtp) REVERT: A 488 LEU cc_start: 0.9382 (tp) cc_final: 0.9141 (tp) REVERT: A 540 LEU cc_start: 0.9448 (tp) cc_final: 0.9149 (tp) REVERT: A 577 ASP cc_start: 0.8891 (t70) cc_final: 0.8655 (t0) REVERT: A 606 ILE cc_start: 0.9502 (mp) cc_final: 0.9283 (tp) REVERT: A 652 HIS cc_start: 0.9092 (t70) cc_final: 0.8428 (t70) REVERT: A 654 TYR cc_start: 0.8488 (m-80) cc_final: 0.7557 (m-10) REVERT: A 677 TYR cc_start: 0.8726 (m-80) cc_final: 0.8272 (m-80) REVERT: A 701 ASP cc_start: 0.8553 (p0) cc_final: 0.8285 (p0) REVERT: A 713 PHE cc_start: 0.8636 (m-80) cc_final: 0.8382 (m-80) REVERT: B 363 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8773 (tp40) REVERT: B 387 PHE cc_start: 0.9131 (t80) cc_final: 0.8805 (t80) REVERT: B 451 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6904 (pm20) REVERT: B 481 MET cc_start: 0.8014 (mtp) cc_final: 0.7553 (mtp) REVERT: B 488 LEU cc_start: 0.9239 (tp) cc_final: 0.8933 (tp) REVERT: B 504 GLU cc_start: 0.9233 (mt-10) cc_final: 0.9014 (pt0) REVERT: B 521 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8923 (tt) REVERT: B 582 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8809 (mmtm) REVERT: B 584 LEU cc_start: 0.9233 (mt) cc_final: 0.9020 (mt) REVERT: B 601 MET cc_start: 0.8163 (ppp) cc_final: 0.7718 (ptt) REVERT: B 606 ILE cc_start: 0.9494 (mp) cc_final: 0.9288 (tp) REVERT: B 616 PHE cc_start: 0.8115 (t80) cc_final: 0.7906 (t80) REVERT: B 620 CYS cc_start: 0.9165 (m) cc_final: 0.8922 (m) REVERT: B 654 TYR cc_start: 0.8375 (m-80) cc_final: 0.8046 (m-10) REVERT: B 677 TYR cc_start: 0.8784 (m-80) cc_final: 0.8350 (m-80) outliers start: 12 outliers final: 8 residues processed: 208 average time/residue: 0.2151 time to fit residues: 56.3499 Evaluate side-chains 146 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.0170 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 556 GLN A 565 HIS A 607 HIS A 621 ASN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 369 GLN B 449 GLN B 556 GLN B 565 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 HIS B 621 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS ** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6594 Z= 0.277 Angle : 0.661 7.740 8928 Z= 0.347 Chirality : 0.043 0.146 1046 Planarity : 0.005 0.039 1170 Dihedral : 5.129 18.252 918 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.94 % 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: -3.12 (0.27), residues: 856 helix: -0.34 (0.26), residues: 356 sheet: -2.86 (0.40), residues: 146 loop : -3.58 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 748 HIS 0.007 0.001 HIS A 565 PHE 0.014 0.002 PHE B 760 TYR 0.005 0.001 TYR B 677 ARG 0.005 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8909 (mpp) cc_final: 0.8700 (mpp) REVERT: A 387 PHE cc_start: 0.9115 (t80) cc_final: 0.8894 (t80) REVERT: A 389 LEU cc_start: 0.9438 (pp) cc_final: 0.9198 (mp) REVERT: A 481 MET cc_start: 0.8098 (mtp) cc_final: 0.7671 (mtp) REVERT: A 488 LEU cc_start: 0.9376 (tp) cc_final: 0.9127 (tp) REVERT: A 574 ILE cc_start: 0.9596 (mt) cc_final: 0.9153 (tp) REVERT: A 575 ASP cc_start: 0.9044 (t0) cc_final: 0.8610 (t0) REVERT: A 677 TYR cc_start: 0.8612 (m-80) cc_final: 0.8049 (m-80) REVERT: B 387 PHE cc_start: 0.8981 (t80) cc_final: 0.8626 (t80) REVERT: B 481 MET cc_start: 0.8125 (mtp) cc_final: 0.7781 (mtp) REVERT: B 488 LEU cc_start: 0.9223 (tp) cc_final: 0.8891 (tp) REVERT: B 536 ASN cc_start: 0.8065 (m-40) cc_final: 0.7831 (m-40) REVERT: B 575 ASP cc_start: 0.8957 (t0) cc_final: 0.8459 (t0) REVERT: B 584 LEU cc_start: 0.9152 (mt) cc_final: 0.8914 (mt) REVERT: B 601 MET cc_start: 0.8215 (ppp) cc_final: 0.7822 (tmm) REVERT: B 654 TYR cc_start: 0.8439 (m-80) cc_final: 0.6852 (m-10) REVERT: B 677 TYR cc_start: 0.8681 (m-80) cc_final: 0.8111 (m-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1701 time to fit residues: 42.3474 Evaluate side-chains 146 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 497 HIS A 499 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 499 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6594 Z= 0.247 Angle : 0.614 5.377 8928 Z= 0.323 Chirality : 0.043 0.155 1046 Planarity : 0.004 0.051 1170 Dihedral : 4.819 18.278 918 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.18 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.29), residues: 856 helix: 0.23 (0.28), residues: 356 sheet: -2.42 (0.43), residues: 136 loop : -3.24 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 748 HIS 0.003 0.001 HIS A 707 PHE 0.017 0.002 PHE B 387 TYR 0.007 0.001 TYR A 654 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 MET cc_start: 0.8070 (mtp) cc_final: 0.7620 (mtp) REVERT: A 488 LEU cc_start: 0.9357 (tp) cc_final: 0.9094 (tp) REVERT: A 504 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8986 (mt-10) REVERT: A 574 ILE cc_start: 0.9617 (mt) cc_final: 0.9177 (tp) REVERT: A 575 ASP cc_start: 0.9027 (t0) cc_final: 0.8604 (t0) REVERT: A 677 TYR cc_start: 0.8565 (m-80) cc_final: 0.8004 (m-80) REVERT: B 389 LEU cc_start: 0.8811 (mp) cc_final: 0.8308 (pp) REVERT: B 451 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 481 MET cc_start: 0.8186 (mtp) cc_final: 0.7761 (mtp) REVERT: B 488 LEU cc_start: 0.9306 (tp) cc_final: 0.8988 (tp) REVERT: B 504 GLU cc_start: 0.9523 (pt0) cc_final: 0.9315 (pp20) REVERT: B 536 ASN cc_start: 0.8173 (m-40) cc_final: 0.7952 (m-40) REVERT: B 558 LEU cc_start: 0.9100 (mt) cc_final: 0.8649 (mt) REVERT: B 575 ASP cc_start: 0.8913 (t0) cc_final: 0.8406 (t0) REVERT: B 582 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8631 (mmmt) REVERT: B 584 LEU cc_start: 0.9177 (mt) cc_final: 0.8956 (mt) REVERT: B 677 TYR cc_start: 0.8678 (m-80) cc_final: 0.8054 (m-80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2147 time to fit residues: 52.9545 Evaluate side-chains 144 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6594 Z= 0.194 Angle : 0.586 7.866 8928 Z= 0.301 Chirality : 0.042 0.141 1046 Planarity : 0.004 0.060 1170 Dihedral : 4.601 17.668 918 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -1.93 (0.29), residues: 856 helix: 0.80 (0.28), residues: 346 sheet: -2.35 (0.43), residues: 136 loop : -2.96 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 748 HIS 0.004 0.001 HIS A 559 PHE 0.013 0.001 PHE A 387 TYR 0.008 0.001 TYR A 654 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 MET cc_start: 0.8001 (mtp) cc_final: 0.7566 (mtp) REVERT: A 488 LEU cc_start: 0.9415 (tp) cc_final: 0.9147 (tp) REVERT: A 574 ILE cc_start: 0.9630 (mt) cc_final: 0.9181 (tp) REVERT: A 575 ASP cc_start: 0.8786 (t0) cc_final: 0.8404 (t0) REVERT: A 601 MET cc_start: 0.7865 (tmm) cc_final: 0.7470 (ptm) REVERT: A 603 THR cc_start: 0.9250 (t) cc_final: 0.8733 (t) REVERT: A 677 TYR cc_start: 0.8514 (m-80) cc_final: 0.7980 (m-80) REVERT: B 389 LEU cc_start: 0.8917 (mp) cc_final: 0.8466 (pp) REVERT: B 481 MET cc_start: 0.8111 (mtp) cc_final: 0.7636 (mtp) REVERT: B 488 LEU cc_start: 0.9283 (tp) cc_final: 0.8968 (tp) REVERT: B 504 GLU cc_start: 0.9541 (pt0) cc_final: 0.9241 (pp20) REVERT: B 507 LYS cc_start: 0.9591 (mtpp) cc_final: 0.9302 (mmtt) REVERT: B 575 ASP cc_start: 0.8844 (t0) cc_final: 0.8399 (t0) REVERT: B 584 LEU cc_start: 0.9133 (mt) cc_final: 0.8915 (mt) REVERT: B 660 CYS cc_start: 0.8452 (m) cc_final: 0.7861 (m) REVERT: B 677 TYR cc_start: 0.8627 (m-80) cc_final: 0.7952 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1501 time to fit residues: 36.2710 Evaluate side-chains 145 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 681 HIS A 755 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 681 HIS B 755 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6594 Z= 0.251 Angle : 0.598 6.744 8928 Z= 0.311 Chirality : 0.042 0.145 1046 Planarity : 0.004 0.063 1170 Dihedral : 4.565 16.787 918 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.96 (0.29), residues: 856 helix: 0.60 (0.28), residues: 358 sheet: -2.20 (0.43), residues: 134 loop : -2.97 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 748 HIS 0.003 0.001 HIS A 707 PHE 0.012 0.002 PHE A 713 TYR 0.009 0.001 TYR A 654 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9274 (t80) cc_final: 0.8896 (t80) REVERT: A 481 MET cc_start: 0.8115 (mtp) cc_final: 0.7569 (mtp) REVERT: A 488 LEU cc_start: 0.9271 (tp) cc_final: 0.8956 (tp) REVERT: A 504 GLU cc_start: 0.8982 (pp20) cc_final: 0.8586 (pp20) REVERT: A 574 ILE cc_start: 0.9646 (mt) cc_final: 0.9170 (tp) REVERT: A 575 ASP cc_start: 0.8879 (t0) cc_final: 0.8453 (t0) REVERT: A 601 MET cc_start: 0.7893 (tmm) cc_final: 0.7526 (ptm) REVERT: A 603 THR cc_start: 0.9265 (t) cc_final: 0.8856 (t) REVERT: A 654 TYR cc_start: 0.7024 (m-10) cc_final: 0.6662 (m-10) REVERT: A 660 CYS cc_start: 0.8167 (m) cc_final: 0.7781 (m) REVERT: A 677 TYR cc_start: 0.8565 (m-80) cc_final: 0.7992 (m-80) REVERT: B 389 LEU cc_start: 0.9006 (mp) cc_final: 0.8706 (pp) REVERT: B 481 MET cc_start: 0.8081 (mtp) cc_final: 0.7648 (mtp) REVERT: B 488 LEU cc_start: 0.9277 (tp) cc_final: 0.8956 (tp) REVERT: B 558 LEU cc_start: 0.9112 (mt) cc_final: 0.8785 (mt) REVERT: B 575 ASP cc_start: 0.8916 (t0) cc_final: 0.8454 (t0) REVERT: B 584 LEU cc_start: 0.9174 (mt) cc_final: 0.8972 (mt) REVERT: B 651 LYS cc_start: 0.9454 (mttm) cc_final: 0.9124 (mmtm) REVERT: B 660 CYS cc_start: 0.8391 (m) cc_final: 0.7971 (m) REVERT: B 677 TYR cc_start: 0.8679 (m-80) cc_final: 0.7963 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1507 time to fit residues: 34.7625 Evaluate side-chains 138 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6594 Z= 0.254 Angle : 0.601 5.978 8928 Z= 0.312 Chirality : 0.042 0.149 1046 Planarity : 0.004 0.065 1170 Dihedral : 4.596 16.540 918 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.91 (0.29), residues: 856 helix: 0.63 (0.28), residues: 358 sheet: -2.29 (0.42), residues: 136 loop : -2.87 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 748 HIS 0.004 0.001 HIS B 707 PHE 0.009 0.002 PHE B 387 TYR 0.008 0.001 TYR B 654 ARG 0.003 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9292 (t80) cc_final: 0.8869 (t80) REVERT: A 481 MET cc_start: 0.7991 (mtp) cc_final: 0.7588 (mtp) REVERT: A 488 LEU cc_start: 0.9233 (tp) cc_final: 0.8902 (tp) REVERT: A 504 GLU cc_start: 0.9024 (pp20) cc_final: 0.8536 (pp20) REVERT: A 574 ILE cc_start: 0.9636 (mt) cc_final: 0.9163 (tp) REVERT: A 575 ASP cc_start: 0.8933 (t0) cc_final: 0.8514 (t0) REVERT: A 601 MET cc_start: 0.7956 (tmm) cc_final: 0.7685 (ptm) REVERT: A 654 TYR cc_start: 0.6950 (m-10) cc_final: 0.6634 (m-10) REVERT: A 660 CYS cc_start: 0.8136 (m) cc_final: 0.7772 (m) REVERT: A 677 TYR cc_start: 0.8526 (m-80) cc_final: 0.7966 (m-80) REVERT: B 481 MET cc_start: 0.8044 (mtp) cc_final: 0.7669 (mtp) REVERT: B 488 LEU cc_start: 0.9223 (tp) cc_final: 0.8884 (tp) REVERT: B 504 GLU cc_start: 0.9167 (pp20) cc_final: 0.8942 (pp20) REVERT: B 558 LEU cc_start: 0.9118 (mt) cc_final: 0.8798 (mt) REVERT: B 575 ASP cc_start: 0.8943 (t0) cc_final: 0.8514 (t0) REVERT: B 584 LEU cc_start: 0.9153 (mt) cc_final: 0.8930 (mt) REVERT: B 660 CYS cc_start: 0.8345 (m) cc_final: 0.7940 (m) REVERT: B 677 TYR cc_start: 0.8694 (m-80) cc_final: 0.8082 (m-80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1455 time to fit residues: 33.6345 Evaluate side-chains 136 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6594 Z= 0.167 Angle : 0.580 5.861 8928 Z= 0.299 Chirality : 0.042 0.162 1046 Planarity : 0.004 0.064 1170 Dihedral : 4.343 16.160 918 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -1.70 (0.29), residues: 856 helix: 0.95 (0.29), residues: 346 sheet: -2.34 (0.41), residues: 146 loop : -2.73 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 748 HIS 0.002 0.001 HIS A 497 PHE 0.023 0.002 PHE B 616 TYR 0.007 0.001 TYR B 654 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9177 (t80) cc_final: 0.8849 (t80) REVERT: A 389 LEU cc_start: 0.9357 (pp) cc_final: 0.8994 (mm) REVERT: A 481 MET cc_start: 0.7978 (mtp) cc_final: 0.7636 (mtp) REVERT: A 488 LEU cc_start: 0.9229 (tp) cc_final: 0.8935 (tp) REVERT: A 504 GLU cc_start: 0.8983 (pp20) cc_final: 0.8708 (pp20) REVERT: A 574 ILE cc_start: 0.9587 (mt) cc_final: 0.9112 (tp) REVERT: A 575 ASP cc_start: 0.8837 (t0) cc_final: 0.8519 (t0) REVERT: A 601 MET cc_start: 0.7967 (tmm) cc_final: 0.7629 (ptm) REVERT: A 603 THR cc_start: 0.9133 (t) cc_final: 0.8932 (t) REVERT: A 654 TYR cc_start: 0.6814 (m-10) cc_final: 0.6552 (m-10) REVERT: A 660 CYS cc_start: 0.8022 (m) cc_final: 0.7747 (m) REVERT: A 677 TYR cc_start: 0.8419 (m-80) cc_final: 0.7920 (m-80) REVERT: B 389 LEU cc_start: 0.8866 (mm) cc_final: 0.8441 (pp) REVERT: B 481 MET cc_start: 0.8104 (mtp) cc_final: 0.7684 (mtp) REVERT: B 488 LEU cc_start: 0.9284 (tp) cc_final: 0.9021 (tp) REVERT: B 575 ASP cc_start: 0.8836 (t0) cc_final: 0.8441 (t0) REVERT: B 651 LYS cc_start: 0.9483 (mttm) cc_final: 0.9142 (mptt) REVERT: B 660 CYS cc_start: 0.8220 (m) cc_final: 0.7779 (m) REVERT: B 677 TYR cc_start: 0.8615 (m-80) cc_final: 0.8083 (m-80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1573 time to fit residues: 37.3845 Evaluate side-chains 138 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6594 Z= 0.201 Angle : 0.638 9.509 8928 Z= 0.324 Chirality : 0.043 0.150 1046 Planarity : 0.004 0.062 1170 Dihedral : 4.361 15.624 918 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.59 (0.29), residues: 856 helix: 0.78 (0.28), residues: 346 sheet: -1.88 (0.44), residues: 132 loop : -2.57 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 748 HIS 0.003 0.001 HIS A 497 PHE 0.008 0.001 PHE A 713 TYR 0.007 0.001 TYR B 654 ARG 0.003 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LEU cc_start: 0.9353 (pp) cc_final: 0.9000 (mm) REVERT: A 481 MET cc_start: 0.7983 (mtp) cc_final: 0.7610 (mtp) REVERT: A 488 LEU cc_start: 0.9290 (tp) cc_final: 0.8959 (tp) REVERT: A 575 ASP cc_start: 0.8809 (t0) cc_final: 0.8538 (t0) REVERT: A 601 MET cc_start: 0.7925 (tmm) cc_final: 0.7586 (ptm) REVERT: A 654 TYR cc_start: 0.6876 (m-10) cc_final: 0.6616 (m-10) REVERT: A 660 CYS cc_start: 0.8058 (m) cc_final: 0.7699 (m) REVERT: A 677 TYR cc_start: 0.8470 (m-80) cc_final: 0.8022 (m-80) REVERT: B 353 GLU cc_start: 0.8653 (mp0) cc_final: 0.8444 (mp0) REVERT: B 389 LEU cc_start: 0.8886 (mm) cc_final: 0.8572 (pp) REVERT: B 481 MET cc_start: 0.8083 (mtp) cc_final: 0.7685 (mtp) REVERT: B 488 LEU cc_start: 0.9250 (tp) cc_final: 0.8906 (tp) REVERT: B 534 MET cc_start: 0.8619 (tpp) cc_final: 0.8146 (tpp) REVERT: B 575 ASP cc_start: 0.8793 (t0) cc_final: 0.8435 (t0) REVERT: B 660 CYS cc_start: 0.8225 (m) cc_final: 0.7785 (m) REVERT: B 677 TYR cc_start: 0.8627 (m-80) cc_final: 0.7982 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1584 time to fit residues: 35.1185 Evaluate side-chains 134 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 639 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6594 Z= 0.363 Angle : 0.716 7.526 8928 Z= 0.373 Chirality : 0.045 0.152 1046 Planarity : 0.005 0.063 1170 Dihedral : 4.841 15.615 918 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.03 (0.29), residues: 856 helix: 0.30 (0.28), residues: 370 sheet: -2.23 (0.41), residues: 142 loop : -2.81 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 768 HIS 0.007 0.001 HIS A 517 PHE 0.020 0.002 PHE B 616 TYR 0.011 0.002 TYR B 654 ARG 0.007 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9248 (t80) cc_final: 0.8587 (t80) REVERT: A 481 MET cc_start: 0.8015 (mtp) cc_final: 0.7668 (mtp) REVERT: A 488 LEU cc_start: 0.9176 (tp) cc_final: 0.8826 (tp) REVERT: A 504 GLU cc_start: 0.8908 (pp20) cc_final: 0.8547 (pp20) REVERT: A 575 ASP cc_start: 0.8947 (t0) cc_final: 0.8521 (t0) REVERT: A 601 MET cc_start: 0.8103 (tmm) cc_final: 0.7006 (tmm) REVERT: A 654 TYR cc_start: 0.7060 (m-10) cc_final: 0.6796 (m-10) REVERT: A 660 CYS cc_start: 0.8179 (m) cc_final: 0.7893 (m) REVERT: A 677 TYR cc_start: 0.8636 (m-80) cc_final: 0.7986 (m-80) REVERT: B 389 LEU cc_start: 0.8958 (mm) cc_final: 0.8643 (pp) REVERT: B 481 MET cc_start: 0.8175 (mtp) cc_final: 0.7786 (mtp) REVERT: B 488 LEU cc_start: 0.9121 (tp) cc_final: 0.8793 (tp) REVERT: B 503 MET cc_start: 0.9095 (mmm) cc_final: 0.8644 (mmm) REVERT: B 534 MET cc_start: 0.8700 (tpp) cc_final: 0.8235 (tpp) REVERT: B 575 ASP cc_start: 0.9001 (t0) cc_final: 0.8591 (t0) REVERT: B 622 MET cc_start: 0.9093 (tpt) cc_final: 0.8634 (tpt) REVERT: B 677 TYR cc_start: 0.8708 (m-80) cc_final: 0.8078 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1543 time to fit residues: 35.0763 Evaluate side-chains 128 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 499 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6594 Z= 0.176 Angle : 0.627 8.381 8928 Z= 0.321 Chirality : 0.044 0.148 1046 Planarity : 0.004 0.058 1170 Dihedral : 4.471 15.559 918 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.61 (0.29), residues: 856 helix: 0.86 (0.29), residues: 346 sheet: -2.08 (0.41), residues: 142 loop : -2.59 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 748 HIS 0.003 0.001 HIS A 497 PHE 0.015 0.001 PHE B 642 TYR 0.006 0.001 TYR A 654 ARG 0.008 0.000 ARG B 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8812 (t80) cc_final: 0.8548 (t80) REVERT: A 389 LEU cc_start: 0.9305 (pp) cc_final: 0.8953 (mm) REVERT: A 488 LEU cc_start: 0.9119 (tp) cc_final: 0.8758 (tp) REVERT: A 504 GLU cc_start: 0.8888 (pp20) cc_final: 0.8617 (pp20) REVERT: A 575 ASP cc_start: 0.8822 (t0) cc_final: 0.8543 (t0) REVERT: A 601 MET cc_start: 0.7897 (tmm) cc_final: 0.7583 (ptm) REVERT: A 654 TYR cc_start: 0.6796 (m-10) cc_final: 0.6531 (m-10) REVERT: A 677 TYR cc_start: 0.8411 (m-80) cc_final: 0.7937 (m-80) REVERT: B 488 LEU cc_start: 0.9182 (tp) cc_final: 0.8878 (tp) REVERT: B 503 MET cc_start: 0.9071 (mmm) cc_final: 0.8590 (mmm) REVERT: B 575 ASP cc_start: 0.8893 (t0) cc_final: 0.8521 (t0) REVERT: B 622 MET cc_start: 0.8970 (tpt) cc_final: 0.8517 (tpt) REVERT: B 677 TYR cc_start: 0.8522 (m-80) cc_final: 0.8010 (m-80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1539 time to fit residues: 37.5861 Evaluate side-chains 141 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076421 restraints weight = 20049.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079177 restraints weight = 12852.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081179 restraints weight = 9299.499| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.170 Angle : 0.619 8.130 8928 Z= 0.314 Chirality : 0.043 0.144 1046 Planarity : 0.004 0.061 1170 Dihedral : 4.301 15.686 918 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.43 (0.30), residues: 856 helix: 0.96 (0.29), residues: 358 sheet: -1.97 (0.42), residues: 142 loop : -2.56 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 748 HIS 0.003 0.001 HIS A 497 PHE 0.025 0.002 PHE B 616 TYR 0.007 0.001 TYR A 654 ARG 0.006 0.000 ARG B 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1654.04 seconds wall clock time: 31 minutes 4.36 seconds (1864.36 seconds total)