Starting phenix.real_space_refine on Sat Aug 3 12:07:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/08_2024/8r33_18859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/08_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_18859/08_2024/8r33_18859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/08_2024/8r33_18859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/08_2024/8r33_18859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r33_18859/08_2024/8r33_18859.cif" } 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-5409/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: 8.22, per 1000 atoms: 1.02 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 52 helices and 2 sheets defined 79.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 Processing helix chain 'A' and resid 458 through 474 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.831A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 Processing helix chain 'A' and resid 519 through 533 removed outlier: 4.001A pdb=" N VAL A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) 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 535 through 555 removed outlier: 3.676A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 646 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 707 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 712 through 718 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.803A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.515A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.778A pdb=" N PHE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 797 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 843 through 874 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 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.535A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 474 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.666A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.748A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 567 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 619 through 646 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.813A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 720 through 741 removed outlier: 3.836A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.724A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 777 removed outlier: 3.706A pdb=" N PHE B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 797 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 814 Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 843 through 874 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=AA1, 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=AA2, 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) 531 hydrogen bonds defined for protein. 1593 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: 2.33 Time building geometry restraints manager: 3.70 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: 383 2.72 - 3.26: 8307 3.26 - 3.81: 14416 3.81 - 4.35: 18964 4.35 - 4.90: 29769 Nonbonded interactions: 71839 Sorted by model distance: nonbonded pdb=" OD1 ASN B 606 " pdb=" O HOH B1001 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN A 606 " pdb=" O HOH A1001 " model vdw 2.185 3.040 nonbonded pdb=" O TRP B 498 " pdb=" O HOH B1002 " model vdw 2.194 3.040 nonbonded pdb=" O SER A 565 " pdb=" OG SER A 568 " model vdw 2.204 3.040 nonbonded pdb=" O TRP A 498 " pdb=" O HOH A1002 " model vdw 2.204 3.040 ... (remaining 71834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 10.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.250 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- 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= 0.181 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 : 0.940 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: 1.3081 time to fit residues: 148.4656 Evaluate side-chains 104 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN 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: 0.8499 moved from start: 0.0982 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= 0.214 Angle : 0.567 5.167 10634 Z= 0.297 Chirality : 0.039 0.144 1270 Planarity : 0.004 0.044 1238 Dihedral : 15.392 80.741 1389 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 18.26 % Favored : 78.72 % 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: 1.98 (0.19), residues: 724 sheet: -0.07 (1.05), residues: 24 loop : -0.11 (0.38), residues: 222 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 0.025 0.002 PHE B 643 TYR 0.015 0.002 TYR A 518 ARG 0.002 0.000 ARG A 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 113 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.874 Fit side-chains REVERT: A 497 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8169 (mtm) REVERT: B 647 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7525 (mppt) REVERT: B 748 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8018 (ttmm) outliers start: 24 outliers final: 9 residues processed: 109 average time/residue: 1.3229 time to fit residues: 152.6366 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 402 ASN 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 748 LYS 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: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7890 Z= 0.362 Angle : 0.670 7.907 10634 Z= 0.348 Chirality : 0.045 0.159 1270 Planarity : 0.005 0.044 1238 Dihedral : 15.753 70.577 1374 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 18.51 % Favored : 78.97 % 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: 1.83 (0.27), residues: 970 helix: 1.68 (0.19), residues: 726 sheet: -0.02 (1.00), residues: 24 loop : -0.07 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 721 HIS 0.012 0.002 HIS A 439 PHE 0.025 0.002 PHE B 643 TYR 0.023 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 110 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.927 Fit side-chains REVERT: A 840 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: B 647 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7565 (mppt) outliers start: 20 outliers final: 8 residues processed: 107 average time/residue: 1.3158 time to fit residues: 149.1094 Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR 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: 0.0970 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.206 Angle : 0.563 5.555 10634 Z= 0.291 Chirality : 0.039 0.146 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.811 63.143 1372 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.14 % Allowed : 18.39 % Favored : 79.47 % 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: 2.22 (0.27), residues: 970 helix: 1.96 (0.19), residues: 728 sheet: 0.16 (1.04), residues: 24 loop : 0.08 (0.41), residues: 218 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 0.025 0.001 PHE B 643 TYR 0.016 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 107 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.926 Fit side-chains REVERT: A 651 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 845 MET cc_start: 0.8482 (tpp) cc_final: 0.8277 (tpp) REVERT: B 845 MET cc_start: 0.8521 (tpp) cc_final: 0.8318 (tpp) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 1.2447 time to fit residues: 137.3309 Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 651 THR 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 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: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.214 Angle : 0.557 5.509 10634 Z= 0.289 Chirality : 0.039 0.147 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.502 59.969 1368 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.14 % Allowed : 18.39 % Favored : 79.47 % 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: 2.28 (0.27), residues: 970 helix: 2.00 (0.19), residues: 728 sheet: 0.07 (1.03), residues: 24 loop : 0.11 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.007 0.002 HIS A 439 PHE 0.025 0.001 PHE B 643 TYR 0.018 0.001 TYR A 518 ARG 0.001 0.000 ARG A 840 *********************** 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 107 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.937 Fit side-chains REVERT: A 651 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 770 MET cc_start: 0.8133 (mtp) cc_final: 0.7810 (mtm) REVERT: B 647 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7538 (mppt) REVERT: B 651 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7904 (p) REVERT: B 770 MET cc_start: 0.8260 (mtp) cc_final: 0.8058 (mtp) outliers start: 17 outliers final: 7 residues processed: 104 average time/residue: 1.2931 time to fit residues: 142.6834 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU 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 786 ILE 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: 2.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1332 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= 0.222 Angle : 0.564 5.773 10634 Z= 0.292 Chirality : 0.039 0.148 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.359 59.559 1368 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 18.14 % Favored : 79.35 % 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: 2.27 (0.27), residues: 970 helix: 1.99 (0.19), residues: 728 sheet: 0.04 (1.03), residues: 24 loop : 0.10 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.025 0.001 PHE B 643 TYR 0.018 0.001 TYR B 518 ARG 0.001 0.000 ARG A 840 *********************** 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 109 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.947 Fit side-chains REVERT: A 402 ASN cc_start: 0.5676 (OUTLIER) cc_final: 0.5456 (p0) REVERT: A 651 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 647 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7545 (mppt) REVERT: B 651 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 770 MET cc_start: 0.8258 (mtp) cc_final: 0.8035 (mtp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.3423 time to fit residues: 151.0031 Evaluate side-chains 102 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR 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: 3.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7890 Z= 0.271 Angle : 0.595 6.409 10634 Z= 0.308 Chirality : 0.041 0.153 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.500 59.496 1368 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.02 % Allowed : 18.77 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.27), residues: 970 helix: 1.93 (0.19), residues: 726 sheet: 0.03 (1.02), residues: 24 loop : 0.03 (0.40), residues: 220 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 0.020 0.002 TYR A 518 ARG 0.001 0.000 ARG A 836 *********************** 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 106 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.965 Fit side-chains REVERT: A 651 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 770 MET cc_start: 0.8205 (mtp) cc_final: 0.7801 (mtm) REVERT: B 647 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7552 (mppt) REVERT: B 770 MET cc_start: 0.8259 (mtp) cc_final: 0.8034 (mtp) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 1.2554 time to fit residues: 137.1613 Evaluate side-chains 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1345 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= 0.220 Angle : 0.564 6.173 10634 Z= 0.291 Chirality : 0.039 0.147 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.141 59.627 1368 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.14 % Allowed : 18.89 % Favored : 78.97 % 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: 2.30 (0.27), residues: 970 helix: 2.02 (0.19), residues: 728 sheet: 0.06 (1.03), residues: 24 loop : 0.10 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.018 0.001 TYR B 518 ARG 0.001 0.000 ARG B 840 *********************** 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 106 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.899 Fit side-chains REVERT: A 651 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 770 MET cc_start: 0.8221 (mtp) cc_final: 0.7813 (mtm) REVERT: B 647 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7547 (mppt) REVERT: B 651 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7907 (p) REVERT: B 657 LYS cc_start: 0.7204 (mmpt) cc_final: 0.6932 (mmtt) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 1.2793 time to fit residues: 139.8328 Evaluate side-chains 99 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR 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: 4.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.0030 chunk 77 optimal weight: 0.0050 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1493 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= 0.168 Angle : 0.523 5.813 10634 Z= 0.268 Chirality : 0.038 0.137 1270 Planarity : 0.004 0.042 1238 Dihedral : 13.394 59.384 1366 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.39 % Allowed : 19.65 % Favored : 78.97 % 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: 2.59 (0.27), residues: 970 helix: 2.24 (0.19), residues: 726 sheet: 0.22 (1.05), residues: 24 loop : 0.18 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 721 HIS 0.004 0.001 HIS A 439 PHE 0.023 0.001 PHE B 643 TYR 0.013 0.001 TYR B 518 ARG 0.001 0.000 ARG A 836 *********************** 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 100 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.917 Fit side-chains REVERT: A 753 LYS cc_start: 0.7304 (pttt) cc_final: 0.7008 (ptmm) REVERT: A 770 MET cc_start: 0.8165 (mtp) cc_final: 0.7779 (mtm) REVERT: B 647 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7548 (mppt) REVERT: B 651 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 753 LYS cc_start: 0.7336 (pttt) cc_final: 0.7095 (ptmm) REVERT: B 770 MET cc_start: 0.8181 (mtp) cc_final: 0.7777 (mtm) outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 1.3197 time to fit residues: 137.0647 Evaluate side-chains 98 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE 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: 0.8980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1457 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= 0.203 Angle : 0.548 5.767 10634 Z= 0.282 Chirality : 0.039 0.144 1270 Planarity : 0.004 0.042 1238 Dihedral : 13.475 59.228 1364 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.01 % Allowed : 19.40 % Favored : 79.60 % 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: 2.47 (0.27), residues: 970 helix: 2.13 (0.19), residues: 728 sheet: 0.16 (1.05), residues: 24 loop : 0.17 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.018 0.001 TYR B 518 ARG 0.002 0.000 ARG B 840 ********************** 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 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.876 Fit side-chains REVERT: A 753 LYS cc_start: 0.7342 (pttt) cc_final: 0.7054 (ptmm) REVERT: A 770 MET cc_start: 0.8222 (mtp) cc_final: 0.7822 (mtm) REVERT: B 647 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: B 651 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 753 LYS cc_start: 0.7308 (pttt) cc_final: 0.7083 (ptmm) REVERT: B 770 MET cc_start: 0.8221 (mtp) cc_final: 0.7824 (mtm) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 1.3206 time to fit residues: 132.8755 Evaluate side-chains 94 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR 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: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106891 restraints weight = 7929.589| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.27 r_work: 0.3173 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1424 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= 0.223 Angle : 0.567 5.832 10634 Z= 0.292 Chirality : 0.039 0.147 1270 Planarity : 0.004 0.042 1238 Dihedral : 13.597 59.396 1363 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.01 % Allowed : 19.65 % Favored : 79.35 % 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: 2.35 (0.27), residues: 970 helix: 2.07 (0.19), residues: 726 sheet: 0.09 (1.04), residues: 24 loop : 0.10 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.018 0.001 TYR B 518 ARG 0.001 0.000 ARG A 840 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3332.63 seconds wall clock time: 59 minutes 21.75 seconds (3561.75 seconds total)