Starting phenix.real_space_refine on Sat Dec 9 08:28:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vt0_32117/12_2023/7vt0_32117.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 44 5.16 5 C 6690 2.51 5 N 1796 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 681": "OD1" <-> "OD2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B ASP 637": "OD1" <-> "OD2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 685": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 29, 'TRANS': 633} Chain: "B" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 632} Time building chain proxies: 5.90, per 1000 atoms: 0.56 Number of scatterers: 10536 At special positions: 0 Unit cell: (156.02, 100.068, 107.6, 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 44 16.00 O 2006 8.00 N 1796 7.00 C 6690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 473 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 736 " distance=2.05 Simple disulfide: pdb=" SG CYS B 684 " - pdb=" SG CYS B 699 " distance=2.02 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: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 28 sheets defined 3.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.527A pdb=" N ALA A 620 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.955A pdb=" N TYR A 630 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.679A pdb=" N TYR B 258 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 259 " --> pdb=" O ASP B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.564A pdb=" N ASN B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.521A pdb=" N ALA B 620 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 702 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 97 removed outlier: 5.717A pdb=" N GLN A 614 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 95 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A 612 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 599 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 585 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 4.398A pdb=" N VAL A 116 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.818A pdb=" N TYR A 177 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 190 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 188 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.613A pdb=" N ASP A 208 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 210 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 232 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 252 removed outlier: 3.547A pdb=" N SER A 252 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 277 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.819A pdb=" N MET A 307 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.696A pdb=" N TYR A 373 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 372 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB1, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.645A pdb=" N ALA A 506 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 534 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 560 through 561 Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 624 removed outlier: 7.171A pdb=" N VAL A 623 " --> pdb=" O PHE A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 724 Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 97 removed outlier: 5.018A pdb=" N VAL B 92 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN B 616 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 94 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 585 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 110 removed outlier: 4.203A pdb=" N VAL B 116 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 134 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.817A pdb=" N TYR B 177 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 189 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 219 through 222 removed outlier: 4.049A pdb=" N GLN B 245 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 248 through 252 removed outlier: 4.252A pdb=" N SER B 250 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 280 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 276 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B 277 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 303 Processing sheet with id=AC4, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.824A pdb=" N PHE B 360 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 371 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 372 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 414 through 416 Processing sheet with id=AC6, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.767A pdb=" N ALA B 506 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 534 " --> pdb=" O VAL B 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC9, first strand: chain 'B' and resid 623 through 624 removed outlier: 6.982A pdb=" N VAL B 623 " --> pdb=" O PHE B 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 722 through 724 162 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1759 1.27 - 1.41: 2909 1.41 - 1.55: 6071 1.55 - 1.69: 9 1.69 - 1.83: 62 Bond restraints: 10810 Sorted by residual: bond pdb=" CA CYS A 362 " pdb=" C CYS A 362 " ideal model delta sigma weight residual 1.533 1.353 0.180 9.60e-03 1.09e+04 3.53e+02 bond pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 1.523 1.372 0.151 1.27e-02 6.20e+03 1.41e+02 bond pdb=" CA ASN B 662 " pdb=" C ASN B 662 " ideal model delta sigma weight residual 1.522 1.385 0.137 1.38e-02 5.25e+03 9.88e+01 bond pdb=" CA ASP B 667 " pdb=" C ASP B 667 " ideal model delta sigma weight residual 1.523 1.392 0.132 1.34e-02 5.57e+03 9.65e+01 bond pdb=" CA LEU A 386 " pdb=" C LEU A 386 " ideal model delta sigma weight residual 1.521 1.393 0.127 1.30e-02 5.92e+03 9.59e+01 ... (remaining 10805 not shown) Histogram of bond angle deviations from ideal: 83.43 - 94.67: 4 94.67 - 105.92: 289 105.92 - 117.17: 7323 117.17 - 128.42: 6943 128.42 - 139.67: 97 Bond angle restraints: 14656 Sorted by residual: angle pdb=" N HIS A 365 " pdb=" CA HIS A 365 " pdb=" C HIS A 365 " ideal model delta sigma weight residual 111.52 83.43 28.09 1.40e+00 5.10e-01 4.03e+02 angle pdb=" N ASP B 629 " pdb=" CA ASP B 629 " pdb=" C ASP B 629 " ideal model delta sigma weight residual 114.56 100.19 14.37 1.27e+00 6.20e-01 1.28e+02 angle pdb=" C ARG B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta sigma weight residual 119.84 105.74 14.10 1.25e+00 6.40e-01 1.27e+02 angle pdb=" CA GLU B 592 " pdb=" C GLU B 592 " pdb=" N LYS B 593 " ideal model delta sigma weight residual 116.08 103.97 12.11 1.29e+00 6.01e-01 8.82e+01 angle pdb=" N PHE B 666 " pdb=" CA PHE B 666 " pdb=" C PHE B 666 " ideal model delta sigma weight residual 110.80 129.83 -19.03 2.13e+00 2.20e-01 7.98e+01 ... (remaining 14651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5681 17.65 - 35.30: 566 35.30 - 52.95: 109 52.95 - 70.59: 37 70.59 - 88.24: 4 Dihedral angle restraints: 6397 sinusoidal: 2557 harmonic: 3840 Sorted by residual: dihedral pdb=" CB CYS B 684 " pdb=" SG CYS B 684 " pdb=" SG CYS B 699 " pdb=" CB CYS B 699 " ideal model delta sinusoidal sigma weight residual -86.00 -19.23 -66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 736 " pdb=" CB CYS A 736 " ideal model delta sinusoidal sigma weight residual 93.00 36.45 56.55 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual -86.00 -32.48 -53.52 1 1.00e+01 1.00e-02 3.89e+01 ... (remaining 6394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1329 0.078 - 0.155: 188 0.155 - 0.233: 23 0.233 - 0.311: 8 0.311 - 0.388: 6 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA ASN A 388 " pdb=" N ASN A 388 " pdb=" C ASN A 388 " pdb=" CB ASN A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA SER A 364 " pdb=" N SER A 364 " pdb=" C SER A 364 " pdb=" CB SER A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA LEU B 645 " pdb=" N LEU B 645 " pdb=" C LEU B 645 " pdb=" CB LEU B 645 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1551 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 674 " -0.033 2.00e-02 2.50e+03 6.62e-02 4.38e+01 pdb=" C ASN B 674 " 0.114 2.00e-02 2.50e+03 pdb=" O ASN B 674 " -0.043 2.00e-02 2.50e+03 pdb=" N CYS B 675 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 592 " -0.018 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C GLU B 592 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 592 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 593 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 673 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 673 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 673 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 674 " -0.023 2.00e-02 2.50e+03 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 485 2.68 - 3.24: 9871 3.24 - 3.79: 14869 3.79 - 4.35: 20121 4.35 - 4.90: 33649 Nonbonded interactions: 78995 Sorted by model distance: nonbonded pdb=" CB VAL A 363 " pdb=" N SER A 364 " model vdw 2.126 2.840 nonbonded pdb=" OE2 GLU B 356 " pdb=" OH TYR B 424 " model vdw 2.196 2.440 nonbonded pdb=" OG SER B 170 " pdb=" O ASP B 173 " model vdw 2.206 2.440 nonbonded pdb=" O LYS A 260 " pdb=" OG1 THR A 263 " model vdw 2.227 2.440 nonbonded pdb=" O GLU A 697 " pdb=" OH TYR A 728 " model vdw 2.229 2.440 ... (remaining 78990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 7.620 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.130 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.011 0.180 10810 Z= 0.733 Angle : 1.309 28.095 14656 Z= 0.802 Chirality : 0.061 0.388 1554 Planarity : 0.007 0.090 1910 Dihedral : 14.914 88.243 3920 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 3.10 % Allowed : 14.30 % Favored : 82.60 % Rotamer: Outliers : 3.65 % Allowed : 3.13 % Favored : 93.22 % Cbeta Deviations : 1.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -4.14 (0.21), residues: 1322 helix: -5.13 (0.27), residues: 6 sheet: -2.70 (0.28), residues: 327 loop : -2.99 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 542 HIS 0.011 0.001 HIS B 545 PHE 0.043 0.002 PHE B 661 TYR 0.024 0.002 TYR B 630 ARG 0.008 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.222 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 164 average time/residue: 0.2406 time to fit residues: 55.2716 Evaluate side-chains 121 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.127 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.1010 time to fit residues: 4.7628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 347 ASN A 388 ASN A 437 ASN ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS B 566 ASN ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10810 Z= 0.223 Angle : 0.716 7.528 14656 Z= 0.381 Chirality : 0.047 0.173 1554 Planarity : 0.005 0.083 1910 Dihedral : 5.764 31.388 1450 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.83 % Favored : 84.04 % Rotamer: Outliers : 1.04 % Allowed : 10.35 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.72 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.28 (0.28), residues: 339 loop : -2.75 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 542 HIS 0.016 0.001 HIS B 608 PHE 0.016 0.001 PHE B 661 TYR 0.019 0.001 TYR B 392 ARG 0.005 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.148 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 0.2001 time to fit residues: 40.6445 Evaluate side-chains 110 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0939 time to fit residues: 2.8496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 269 HIS A 365 HIS ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 614 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10810 Z= 0.453 Angle : 0.824 9.750 14656 Z= 0.435 Chirality : 0.051 0.239 1554 Planarity : 0.005 0.077 1910 Dihedral : 6.394 46.130 1450 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 1.29 % Allowed : 17.93 % Favored : 80.79 % Rotamer: Outliers : 1.74 % Allowed : 13.83 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.76 (0.22), residues: 1322 helix: -5.41 (0.39), residues: 6 sheet: -2.37 (0.28), residues: 340 loop : -2.72 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 542 HIS 0.006 0.002 HIS A 169 PHE 0.020 0.002 PHE B 576 TYR 0.024 0.002 TYR A 563 ARG 0.005 0.001 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.192 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 127 average time/residue: 0.2311 time to fit residues: 42.2108 Evaluate side-chains 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1001 time to fit residues: 3.3315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10810 Z= 0.214 Angle : 0.688 10.028 14656 Z= 0.363 Chirality : 0.046 0.225 1554 Planarity : 0.004 0.072 1910 Dihedral : 5.732 35.477 1450 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 1.36 % Allowed : 12.18 % Favored : 86.46 % Rotamer: Outliers : 1.57 % Allowed : 16.17 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.47 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.07 (0.29), residues: 323 loop : -2.59 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 542 HIS 0.003 0.001 HIS A 169 PHE 0.024 0.002 PHE A 382 TYR 0.019 0.001 TYR B 392 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.200 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 0.2460 time to fit residues: 44.0781 Evaluate side-chains 108 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0923 time to fit residues: 2.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10810 Z= 0.338 Angle : 0.731 9.678 14656 Z= 0.386 Chirality : 0.048 0.231 1554 Planarity : 0.005 0.069 1910 Dihedral : 5.858 34.351 1450 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 1.21 % Allowed : 16.49 % Favored : 82.30 % Rotamer: Outliers : 1.91 % Allowed : 16.96 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.55 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.19 (0.28), residues: 347 loop : -2.61 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 542 HIS 0.005 0.001 HIS A 169 PHE 0.017 0.002 PHE B 200 TYR 0.020 0.002 TYR A 563 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.319 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 117 average time/residue: 0.2602 time to fit residues: 43.2743 Evaluate side-chains 108 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1029 time to fit residues: 3.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 chunk 59 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10810 Z= 0.163 Angle : 0.648 8.120 14656 Z= 0.340 Chirality : 0.045 0.160 1554 Planarity : 0.004 0.066 1910 Dihedral : 5.321 31.956 1450 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 1.13 % Allowed : 11.57 % Favored : 87.29 % Rotamer: Outliers : 0.87 % Allowed : 17.48 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.21 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.84 (0.29), residues: 318 loop : -2.42 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 542 HIS 0.003 0.000 HIS B 545 PHE 0.012 0.001 PHE A 382 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.171 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 122 average time/residue: 0.2309 time to fit residues: 40.5826 Evaluate side-chains 108 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0950 time to fit residues: 2.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10810 Z= 0.191 Angle : 0.657 10.413 14656 Z= 0.343 Chirality : 0.045 0.147 1554 Planarity : 0.004 0.064 1910 Dihedral : 5.278 31.552 1450 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.24 % Favored : 85.70 % Rotamer: Outliers : 1.04 % Allowed : 18.17 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.16 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.79 (0.30), residues: 324 loop : -2.39 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 542 HIS 0.003 0.001 HIS B 169 PHE 0.011 0.001 PHE A 284 TYR 0.013 0.001 TYR B 392 ARG 0.002 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.052 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.2478 time to fit residues: 41.6358 Evaluate side-chains 104 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1060 time to fit residues: 2.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10810 Z= 0.198 Angle : 0.655 9.741 14656 Z= 0.342 Chirality : 0.045 0.141 1554 Planarity : 0.004 0.063 1910 Dihedral : 5.267 31.197 1450 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.63 % Favored : 86.46 % Rotamer: Outliers : 0.61 % Allowed : 18.78 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.06 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.68 (0.30), residues: 315 loop : -2.33 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 542 HIS 0.003 0.001 HIS B 169 PHE 0.011 0.001 PHE B 200 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.186 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 110 average time/residue: 0.2692 time to fit residues: 41.3563 Evaluate side-chains 107 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1078 time to fit residues: 2.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10810 Z= 0.215 Angle : 0.661 9.087 14656 Z= 0.345 Chirality : 0.045 0.137 1554 Planarity : 0.004 0.062 1910 Dihedral : 5.285 30.470 1450 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.83 % Allowed : 13.62 % Favored : 85.55 % Rotamer: Outliers : 0.35 % Allowed : 19.74 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.07 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.71 (0.30), residues: 325 loop : -2.33 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 PHE 0.013 0.001 PHE A 284 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.2649 time to fit residues: 40.1239 Evaluate side-chains 103 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1457 time to fit residues: 2.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10810 Z= 0.307 Angle : 0.711 9.126 14656 Z= 0.371 Chirality : 0.046 0.143 1554 Planarity : 0.004 0.062 1910 Dihedral : 5.638 32.334 1450 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.83 % Allowed : 15.28 % Favored : 83.89 % Rotamer: Outliers : 0.26 % Allowed : 20.17 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.20 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.80 (0.29), residues: 343 loop : -2.43 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 542 HIS 0.005 0.001 HIS A 169 PHE 0.022 0.002 PHE A 382 TYR 0.016 0.002 TYR A 563 ARG 0.004 0.000 ARG B 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 101 average time/residue: 0.3008 time to fit residues: 41.8328 Evaluate side-chains 100 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1152 time to fit residues: 2.2951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.203837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149698 restraints weight = 11909.377| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.31 r_work: 0.3538 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10810 Z= 0.262 Angle : 0.691 8.802 14656 Z= 0.361 Chirality : 0.046 0.147 1554 Planarity : 0.004 0.062 1910 Dihedral : 5.547 28.475 1450 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.83 % Allowed : 14.37 % Favored : 84.80 % Rotamer: Outliers : 0.09 % Allowed : 20.26 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -3.20 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.89 (0.29), residues: 328 loop : -2.39 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 542 HIS 0.004 0.001 HIS A 169 PHE 0.020 0.002 PHE A 382 TYR 0.015 0.001 TYR A 349 ARG 0.016 0.000 ARG B 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.08 seconds wall clock time: 43 minutes 20.24 seconds (2600.24 seconds total)