Starting phenix.real_space_refine on Tue Jun 25 13:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/06_2024/8r33_18859_updated.pdb" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 5202 2.51 5 N 1148 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A ASP 795": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8066 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3677 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3677 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'3PH': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'3PH': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Time building chain proxies: 7.71, per 1000 atoms: 0.96 Number of scatterers: 8066 At special positions: 0 Unit cell: (108.297, 100.275, 74.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 8 15.00 O 1656 8.00 N 1148 7.00 C 5202 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: 3.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 2 sheets defined 70.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 436 through 454 Processing helix chain 'A' and resid 459 through 473 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.593A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.676A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 568 through 571 No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 579 through 597 removed outlier: 4.271A pdb=" N MET A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 645 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 665 through 682 Processing helix chain 'A' and resid 684 through 691 removed outlier: 3.825A pdb=" N GLU A 688 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY A 689 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 691 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 706 removed outlier: 3.973A pdb=" N ILE A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Proline residue: A 701 - end of helix Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 721 through 740 Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.515A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 776 removed outlier: 3.778A pdb=" N PHE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 796 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 802 through 815 removed outlier: 4.220A pdb=" N SER A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 844 through 873 Proline residue: A 853 - end of helix removed outlier: 4.741A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 454 removed outlier: 3.535A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 500 through 517 Processing helix chain 'B' and resid 521 through 532 removed outlier: 3.666A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 554 removed outlier: 3.748A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Proline residue: B 569 - end of helix Processing helix chain 'B' and resid 579 through 597 removed outlier: 4.149A pdb=" N MET B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 665 through 682 Processing helix chain 'B' and resid 688 through 691 No H-bonds generated for 'chain 'B' and resid 688 through 691' Processing helix chain 'B' and resid 694 through 706 removed outlier: 3.536A pdb=" N ILE B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Proline residue: B 701 - end of helix Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 721 through 740 Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.724A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 776 removed outlier: 3.706A pdb=" N PHE B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 796 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 802 through 815 removed outlier: 4.205A pdb=" N SER B 815 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 832 Processing helix chain 'B' and resid 844 through 873 Proline residue: B 853 - end of helix removed outlier: 4.730A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.534A pdb=" N TRP A 387 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 403 " --> pdb=" O TRP A 387 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 384 through 387 removed outlier: 3.509A pdb=" N VAL B 403 " --> pdb=" O TRP B 387 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1347 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: 2.10 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1197 1.33 - 1.45: 1895 1.45 - 1.57: 4704 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7890 Sorted by residual: bond pdb=" N VAL A 403 " pdb=" CA VAL A 403 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.22e-02 6.72e+03 1.35e+00 bond pdb=" N VAL B 403 " pdb=" CA VAL B 403 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.22e-02 6.72e+03 1.34e+00 bond pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.09e-01 bond pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " ideal model delta sigma weight residual 1.531 1.546 -0.015 1.72e-02 3.38e+03 7.69e-01 ... (remaining 7885 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 232 106.58 - 113.44: 4485 113.44 - 120.30: 2750 120.30 - 127.16: 3088 127.16 - 134.02: 79 Bond angle restraints: 10634 Sorted by residual: angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 122.74 -2.41 8.00e-01 1.56e+00 9.11e+00 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 9.01e+00 angle pdb=" C LEU A 642 " pdb=" N PHE A 643 " pdb=" CA PHE A 643 " ideal model delta sigma weight residual 121.94 116.95 4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " pdb=" CD GLU A 513 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.70e+00 3.46e-01 5.96e+00 angle pdb=" C VAL A 466 " pdb=" CA VAL A 466 " pdb=" CB VAL A 466 " ideal model delta sigma weight residual 114.00 110.83 3.17 1.31e+00 5.83e-01 5.85e+00 ... (remaining 10629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4021 18.00 - 36.00: 523 36.00 - 54.00: 194 54.00 - 72.00: 36 72.00 - 89.99: 6 Dihedral angle restraints: 4780 sinusoidal: 1974 harmonic: 2806 Sorted by residual: dihedral pdb=" CA ILE A 785 " pdb=" C ILE A 785 " pdb=" N ILE A 786 " pdb=" CA ILE A 786 " ideal model delta harmonic sigma weight residual -180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 688 " pdb=" CG GLU B 688 " pdb=" CD GLU B 688 " pdb=" OE1 GLU B 688 " ideal model delta sinusoidal sigma weight residual 0.00 -88.26 88.26 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLU A 654 " pdb=" CB GLU A 654 " pdb=" CG GLU A 654 " pdb=" CD GLU A 654 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 780 0.028 - 0.055: 321 0.055 - 0.083: 112 0.083 - 0.111: 51 0.111 - 0.138: 6 Chirality restraints: 1270 Sorted by residual: chirality pdb=" CA PHE A 643 " pdb=" N PHE A 643 " pdb=" C PHE A 643 " pdb=" CB PHE A 643 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE B 457 " pdb=" N ILE B 457 " pdb=" C ILE B 457 " pdb=" CB ILE B 457 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PHE B 643 " pdb=" N PHE B 643 " pdb=" C PHE B 643 " pdb=" CB PHE B 643 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1267 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 457 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 458 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 862 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C VAL A 862 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL A 862 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 863 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 568 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 569 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " 0.020 5.00e-02 4.00e+02 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 386 2.72 - 3.26: 8373 3.26 - 3.81: 14493 3.81 - 4.35: 19114 4.35 - 4.90: 29793 Nonbonded interactions: 72159 Sorted by model distance: nonbonded pdb=" OD1 ASN B 606 " pdb=" O HOH B1001 " model vdw 2.171 2.440 nonbonded pdb=" OD1 ASN A 606 " pdb=" O HOH A1001 " model vdw 2.185 2.440 nonbonded pdb=" O TRP B 498 " pdb=" O HOH B1002 " model vdw 2.194 2.440 nonbonded pdb=" O SER A 565 " pdb=" OG SER A 568 " model vdw 2.204 2.440 nonbonded pdb=" O TRP A 498 " pdb=" O HOH A1002 " model vdw 2.204 2.440 ... (remaining 72154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.190 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: 28.210 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 29.600 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.003 0.031 7890 Z= 0.184 Angle : 0.557 5.617 10634 Z= 0.307 Chirality : 0.037 0.138 1270 Planarity : 0.004 0.047 1238 Dihedral : 18.607 89.995 2972 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 20.53 % Favored : 77.08 % 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: 1.52 (0.26), residues: 970 helix: 1.52 (0.19), residues: 714 sheet: -0.33 (1.04), residues: 24 loop : -0.31 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.021 0.001 PHE A 643 TYR 0.013 0.002 TYR A 518 ARG 0.002 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.944 Fit side-chains REVERT: B 531 PHE cc_start: 0.7542 (t80) cc_final: 0.6387 (m-10) REVERT: B 566 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7992 (tp) outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 1.3284 time to fit residues: 150.5571 Evaluate side-chains 104 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7890 Z= 0.232 Angle : 0.553 5.460 10634 Z= 0.283 Chirality : 0.039 0.145 1270 Planarity : 0.004 0.040 1238 Dihedral : 15.553 82.171 1389 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.65 % Allowed : 18.39 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.27), residues: 970 helix: 1.82 (0.19), residues: 718 sheet: -0.07 (1.04), residues: 24 loop : -0.09 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.024 0.002 PHE B 643 TYR 0.015 0.002 TYR A 518 ARG 0.001 0.000 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.798 Fit side-chains REVERT: B 647 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: B 748 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8029 (ttmm) outliers start: 29 outliers final: 14 residues processed: 115 average time/residue: 1.3015 time to fit residues: 158.3765 Evaluate side-chains 104 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7890 Z= 0.448 Angle : 0.695 8.688 10634 Z= 0.356 Chirality : 0.047 0.166 1270 Planarity : 0.005 0.038 1238 Dihedral : 16.210 74.724 1378 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.90 % Allowed : 18.01 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 970 helix: 1.46 (0.19), residues: 720 sheet: -0.27 (0.97), residues: 24 loop : -0.34 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 721 HIS 0.011 0.002 HIS A 439 PHE 0.024 0.002 PHE B 643 TYR 0.022 0.002 TYR A 518 ARG 0.003 0.001 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.896 Fit side-chains REVERT: B 566 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 647 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7576 (mppt) outliers start: 31 outliers final: 14 residues processed: 113 average time/residue: 1.2976 time to fit residues: 155.7994 Evaluate side-chains 105 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7890 Z= 0.197 Angle : 0.532 5.703 10634 Z= 0.270 Chirality : 0.038 0.145 1270 Planarity : 0.004 0.036 1238 Dihedral : 15.066 66.958 1378 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 19.40 % Favored : 78.09 % 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: 1.94 (0.27), residues: 970 helix: 1.79 (0.19), residues: 720 sheet: 0.06 (1.02), residues: 24 loop : -0.08 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.013 0.001 TYR A 518 ARG 0.001 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.959 Fit side-chains REVERT: A 651 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7934 (p) REVERT: A 757 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: B 651 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7930 (p) REVERT: B 757 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: B 770 MET cc_start: 0.8291 (mtp) cc_final: 0.7987 (mtt) outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 1.3310 time to fit residues: 148.2251 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7890 Z= 0.328 Angle : 0.614 7.369 10634 Z= 0.313 Chirality : 0.042 0.158 1270 Planarity : 0.005 0.036 1238 Dihedral : 15.267 63.712 1368 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.53 % Allowed : 19.14 % Favored : 77.33 % 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: 1.67 (0.27), residues: 970 helix: 1.60 (0.19), residues: 720 sheet: -0.05 (0.98), residues: 24 loop : -0.24 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 721 HIS 0.010 0.002 HIS A 439 PHE 0.024 0.002 PHE B 643 TYR 0.020 0.002 TYR A 518 ARG 0.002 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.886 Fit side-chains REVERT: B 647 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: B 770 MET cc_start: 0.8346 (mtp) cc_final: 0.8123 (mtp) outliers start: 28 outliers final: 12 residues processed: 111 average time/residue: 1.2365 time to fit residues: 145.9547 Evaluate side-chains 101 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7890 Z= 0.307 Angle : 0.602 6.874 10634 Z= 0.307 Chirality : 0.041 0.155 1270 Planarity : 0.004 0.035 1238 Dihedral : 15.056 61.731 1366 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.27 % Allowed : 19.14 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 970 helix: 1.56 (0.19), residues: 724 sheet: -0.07 (0.98), residues: 24 loop : -0.17 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 721 HIS 0.009 0.002 HIS A 439 PHE 0.024 0.002 PHE B 643 TYR 0.019 0.002 TYR B 518 ARG 0.001 0.000 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.852 Fit side-chains REVERT: A 770 MET cc_start: 0.8313 (mtp) cc_final: 0.8006 (mtt) REVERT: B 647 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7615 (mppt) REVERT: B 748 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8099 (ttmm) outliers start: 26 outliers final: 15 residues processed: 108 average time/residue: 1.2741 time to fit residues: 145.9384 Evaluate side-chains 104 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7890 Z= 0.188 Angle : 0.519 6.463 10634 Z= 0.262 Chirality : 0.037 0.140 1270 Planarity : 0.004 0.034 1238 Dihedral : 14.191 59.545 1366 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.78 % Allowed : 18.51 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.27), residues: 970 helix: 1.89 (0.20), residues: 720 sheet: 0.01 (1.01), residues: 24 loop : 0.04 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.005 0.001 HIS A 439 PHE 0.023 0.001 PHE B 643 TYR 0.012 0.001 TYR B 518 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.923 Fit side-chains REVERT: A 651 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 757 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: B 647 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: B 651 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 748 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: B 753 LYS cc_start: 0.7484 (pttt) cc_final: 0.7226 (ptmm) REVERT: B 770 MET cc_start: 0.8293 (mtp) cc_final: 0.7975 (mtt) outliers start: 30 outliers final: 12 residues processed: 112 average time/residue: 1.2059 time to fit residues: 143.4408 Evaluate side-chains 105 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7890 Z= 0.280 Angle : 0.587 6.674 10634 Z= 0.298 Chirality : 0.040 0.153 1270 Planarity : 0.004 0.035 1238 Dihedral : 14.489 59.931 1366 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.90 % Allowed : 19.52 % Favored : 77.58 % 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: 1.85 (0.27), residues: 970 helix: 1.71 (0.19), residues: 722 sheet: -0.04 (1.00), residues: 24 loop : -0.09 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 721 HIS 0.009 0.002 HIS A 439 PHE 0.024 0.002 PHE B 643 TYR 0.018 0.002 TYR B 518 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.880 Fit side-chains REVERT: A 651 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 770 MET cc_start: 0.8318 (mtp) cc_final: 0.7971 (mtm) REVERT: B 647 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: B 651 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7946 (p) REVERT: B 657 LYS cc_start: 0.7272 (mmpt) cc_final: 0.7007 (mmtt) REVERT: B 753 LYS cc_start: 0.7477 (pttt) cc_final: 0.7250 (ptmm) REVERT: B 770 MET cc_start: 0.8317 (mtp) cc_final: 0.8004 (mtt) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 1.2405 time to fit residues: 140.8859 Evaluate side-chains 103 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7890 Z= 0.181 Angle : 0.520 5.827 10634 Z= 0.262 Chirality : 0.037 0.139 1270 Planarity : 0.004 0.035 1238 Dihedral : 13.891 59.864 1366 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.77 % Allowed : 19.77 % Favored : 77.46 % 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: 2.17 (0.27), residues: 970 helix: 1.93 (0.20), residues: 720 sheet: 0.08 (1.02), residues: 24 loop : 0.10 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.005 0.001 HIS A 439 PHE 0.023 0.001 PHE B 643 TYR 0.012 0.001 TYR B 518 ARG 0.001 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.821 Fit side-chains REVERT: A 757 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: A 770 MET cc_start: 0.8279 (mtp) cc_final: 0.7926 (mtm) REVERT: B 647 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7609 (mppt) REVERT: B 748 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8065 (ttmm) REVERT: B 753 LYS cc_start: 0.7493 (pttt) cc_final: 0.7265 (ptmm) REVERT: B 770 MET cc_start: 0.8310 (mtp) cc_final: 0.7983 (mtt) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 1.2249 time to fit residues: 140.7896 Evaluate side-chains 101 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7890 Z= 0.180 Angle : 0.515 6.347 10634 Z= 0.260 Chirality : 0.037 0.140 1270 Planarity : 0.004 0.034 1238 Dihedral : 13.644 59.779 1364 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.64 % Allowed : 20.40 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 970 helix: 1.95 (0.19), residues: 720 sheet: 0.18 (1.03), residues: 24 loop : 0.12 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.013 0.001 TYR B 518 ARG 0.001 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.857 Fit side-chains REVERT: A 753 LYS cc_start: 0.7279 (pttt) cc_final: 0.6985 (ptmm) REVERT: A 770 MET cc_start: 0.8283 (mtp) cc_final: 0.7925 (mtm) REVERT: B 748 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8065 (ttmm) REVERT: B 753 LYS cc_start: 0.7498 (pttt) cc_final: 0.7275 (ptmm) REVERT: B 770 MET cc_start: 0.8318 (mtp) cc_final: 0.7986 (mtt) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 1.3411 time to fit residues: 144.9838 Evaluate side-chains 98 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** 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 = 0.3591 r_free = 0.3591 target = 0.131926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105052 restraints weight = 7793.665| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.24 r_work: 0.3137 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7890 Z= 0.207 Angle : 0.537 6.246 10634 Z= 0.271 Chirality : 0.038 0.144 1270 Planarity : 0.004 0.034 1238 Dihedral : 13.686 59.616 1363 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.51 % Allowed : 20.65 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.27), residues: 970 helix: 1.87 (0.19), residues: 720 sheet: 0.15 (1.02), residues: 24 loop : 0.13 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.015 0.001 TYR B 518 ARG 0.001 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.88 seconds wall clock time: 59 minutes 33.17 seconds (3573.17 seconds total)