Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:23:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/12_2022/7wxh_32879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/12_2022/7wxh_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_32879/12_2022/7wxh_32879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/12_2022/7wxh_32879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/12_2022/7wxh_32879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxh_32879/12_2022/7wxh_32879.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 4.37, per 1000 atoms: 0.67 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 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: 0.41 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: 1.72 Time building geometry restraints manager: 2.82 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 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. 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: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 6.020 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 21.040 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 % 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 *********************** 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 : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 208 average time/residue: 0.2109 time to fit residues: 55.6987 Evaluate side-chains 137 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0597 time to fit residues: 1.9437 ------------------------------------------------------------------------------- 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: 0.0070 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 369 GLN A 556 GLN A 565 HIS A 607 HIS A 621 ASN A 652 HIS A 675 HIS ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN B 556 GLN B 565 HIS B 607 HIS B 621 ASN 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: 0.8057 moved from start: 0.2604 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= 0.195 Angle : 0.631 7.003 8928 Z= 0.328 Chirality : 0.042 0.141 1046 Planarity : 0.004 0.039 1170 Dihedral : 4.945 16.454 918 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.00 % 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: -2.87 (0.27), residues: 856 helix: 0.00 (0.27), residues: 346 sheet: -2.81 (0.40), residues: 146 loop : -3.47 (0.29), residues: 364 *********************** 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 191 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1666 time to fit residues: 42.6508 Evaluate side-chains 142 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1338 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 497 HIS A 499 ASN B 354 ASN B 369 GLN B 497 HIS B 499 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3069 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= 0.196 Angle : 0.600 7.475 8928 Z= 0.313 Chirality : 0.042 0.139 1046 Planarity : 0.004 0.042 1170 Dihedral : 4.666 15.623 918 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer Outliers : 0.00 % 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: -2.25 (0.28), residues: 856 helix: 0.44 (0.28), residues: 358 sheet: -2.33 (0.42), residues: 136 loop : -3.25 (0.29), residues: 362 *********************** 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 175 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1552 time to fit residues: 37.3032 Evaluate side-chains 143 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9846 ------------------------------------------------------------------------------- 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: 0.0030 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 overall best weight: 0.5488 ------------------------------------------------------------------------------- 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: 0.7999 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 6594 Z= 0.153 Angle : 0.578 6.547 8928 Z= 0.296 Chirality : 0.042 0.136 1046 Planarity : 0.004 0.043 1170 Dihedral : 4.383 17.378 918 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.00 % 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: -1.79 (0.29), residues: 856 helix: 1.06 (0.29), residues: 348 sheet: -2.40 (0.41), residues: 144 loop : -3.01 (0.30), residues: 364 *********************** 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 187 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1523 time to fit residues: 39.2208 Evaluate side-chains 142 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0479 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6594 Z= 0.167 Angle : 0.587 7.068 8928 Z= 0.302 Chirality : 0.042 0.134 1046 Planarity : 0.004 0.046 1170 Dihedral : 4.258 17.213 918 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.30), residues: 856 helix: 0.97 (0.29), residues: 348 sheet: -1.93 (0.43), residues: 134 loop : -2.73 (0.31), residues: 374 *********************** 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 179 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1619 time to fit residues: 39.6592 Evaluate side-chains 143 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0878 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.211 Angle : 0.605 6.994 8928 Z= 0.313 Chirality : 0.043 0.152 1046 Planarity : 0.004 0.047 1170 Dihedral : 4.343 16.240 918 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.14 % 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 (0.29), residues: 856 helix: 0.61 (0.28), residues: 358 sheet: -1.97 (0.42), residues: 136 loop : -2.68 (0.31), residues: 362 *********************** 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 171 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.1510 time to fit residues: 35.7892 Evaluate side-chains 141 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0945 time to fit residues: 1.2294 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6594 Z= 0.199 Angle : 0.616 9.883 8928 Z= 0.318 Chirality : 0.043 0.162 1046 Planarity : 0.004 0.046 1170 Dihedral : 4.401 16.263 918 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.00 % 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: -1.68 (0.29), residues: 856 helix: 0.57 (0.28), residues: 358 sheet: -1.94 (0.42), residues: 136 loop : -2.54 (0.31), residues: 362 *********************** 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 169 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1442 time to fit residues: 34.3296 Evaluate side-chains 131 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0460 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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: 0.7998 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6594 Z= 0.154 Angle : 0.622 9.835 8928 Z= 0.317 Chirality : 0.043 0.155 1046 Planarity : 0.004 0.044 1170 Dihedral : 4.196 16.920 918 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 0.00 % 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: -1.51 (0.29), residues: 856 helix: 0.73 (0.29), residues: 358 sheet: -1.91 (0.42), residues: 136 loop : -2.46 (0.31), residues: 362 *********************** 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 171 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.847 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1529 time to fit residues: 36.1883 Evaluate side-chains 139 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0530 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6594 Z= 0.190 Angle : 0.656 10.894 8928 Z= 0.337 Chirality : 0.044 0.151 1046 Planarity : 0.004 0.071 1170 Dihedral : 4.257 18.525 918 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.00 % 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: -1.53 (0.29), residues: 856 helix: 0.62 (0.29), residues: 356 sheet: -1.90 (0.42), residues: 136 loop : -2.35 (0.31), residues: 364 *********************** 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 161 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1528 time to fit residues: 34.8231 Evaluate side-chains 136 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9842 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 78 optimal weight: 0.0020 chunk 68 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4775 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= 0.178 Angle : 0.656 10.560 8928 Z= 0.339 Chirality : 0.044 0.153 1046 Planarity : 0.004 0.060 1170 Dihedral : 4.271 16.144 918 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 0.00 % 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: -1.48 (0.29), residues: 856 helix: 0.61 (0.29), residues: 356 sheet: -1.84 (0.42), residues: 136 loop : -2.27 (0.32), residues: 364 ********************** 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 168 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1474 time to fit residues: 34.6996 Evaluate side-chains 135 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0694 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080062 restraints weight = 19798.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082780 restraints weight = 12992.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084840 restraints weight = 9494.558| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6594 Z= 0.169 Angle : 0.694 11.555 8928 Z= 0.352 Chirality : 0.044 0.153 1046 Planarity : 0.004 0.068 1170 Dihedral : 4.224 17.559 918 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 0.00 % 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: -1.33 (0.30), residues: 856 helix: 0.73 (0.29), residues: 356 sheet: -1.75 (0.43), residues: 136 loop : -2.19 (0.32), residues: 364 =============================================================================== Job complete usr+sys time: 1580.19 seconds wall clock time: 29 minutes 27.62 seconds (1767.62 seconds total)