Starting phenix.real_space_refine on Fri Jul 19 10:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/07_2024/8qa4_18298.cif" } resolution = 2.8 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= 0.013 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 S 10 5.16 5 C 2448 2.51 5 N 614 2.21 5 O 748 1.98 5 H 3724 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 476": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 476": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 535": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7544 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3685 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3685 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 42 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 42 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 5.46, per 1000 atoms: 0.72 Number of scatterers: 7544 At special positions: 0 Unit cell: (106.19, 90.118, 50.512, 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 10 16.00 O 748 8.00 N 614 7.00 C 2448 6.00 H 3724 1.00 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: 6.90 Conformation dependent library (CDL) restraints added in 794.7 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 872 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 44.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.986A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 467 through 476 Processing helix chain 'A' and resid 518 through 530 removed outlier: 3.801A pdb=" N LYS A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.860A pdb=" N MET A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TRP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.738A pdb=" N TYR A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 427 through 440 removed outlier: 3.986A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 467 through 476 Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.802A pdb=" N LYS B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.860A pdb=" N MET B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 616 removed outlier: 3.738A pdb=" N TYR B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 485 removed outlier: 5.311A pdb=" N THR A 481 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 516 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 511 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 542 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 492 removed outlier: 5.102A pdb=" N VAL A 507 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 558 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 574 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR A 560 " --> pdb=" O PRO A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 480 through 485 removed outlier: 5.311A pdb=" N THR B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 516 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 511 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B 542 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU B 546 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 488 through 492 removed outlier: 5.102A pdb=" N VAL B 507 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 558 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 574 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR B 560 " --> pdb=" O PRO B 572 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 471 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: 2.59 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 842 1.05 - 1.24: 3404 1.24 - 1.43: 1290 1.43 - 1.62: 2070 1.62 - 1.81: 16 Bond restraints: 7622 Sorted by residual: bond pdb=" C2 SAH A 701 " pdb=" H2 SAH A 701 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C8 SAH B 701 " pdb=" H8 SAH B 701 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CZ2 TRP B 633 " pdb=" HZ2 TRP B 633 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C8 SAH A 701 " pdb=" H8 SAH A 701 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C2 SAH B 701 " pdb=" H2 SAH B 701 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 7617 not shown) Histogram of bond angle deviations from ideal: 97.15 - 105.01: 349 105.01 - 112.88: 8115 112.88 - 120.74: 3667 120.74 - 128.61: 1509 128.61 - 136.47: 80 Bond angle restraints: 13720 Sorted by residual: angle pdb=" C GLU B 600 " pdb=" N GLU B 601 " pdb=" CA GLU B 601 " ideal model delta sigma weight residual 120.54 132.31 -11.77 1.35e+00 5.49e-01 7.60e+01 angle pdb=" C GLU A 600 " pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 120.54 132.29 -11.75 1.35e+00 5.49e-01 7.58e+01 angle pdb=" CA SAH A 701 " pdb=" C SAH A 701 " pdb=" O SAH A 701 " ideal model delta sigma weight residual 120.80 107.35 13.45 1.70e+00 3.46e-01 6.26e+01 angle pdb=" CA SAH B 701 " pdb=" C SAH B 701 " pdb=" O SAH B 701 " ideal model delta sigma weight residual 120.80 107.39 13.41 1.70e+00 3.46e-01 6.23e+01 angle pdb=" CA ASP B 495 " pdb=" CB ASP B 495 " pdb=" CG ASP B 495 " ideal model delta sigma weight residual 112.60 120.22 -7.62 1.00e+00 1.00e+00 5.80e+01 ... (remaining 13715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.25: 3308 24.25 - 48.50: 158 48.50 - 72.75: 80 72.75 - 96.99: 10 96.99 - 121.24: 4 Dihedral angle restraints: 3560 sinusoidal: 1926 harmonic: 1634 Sorted by residual: dihedral pdb=" C GLU B 602 " pdb=" N GLU B 602 " pdb=" CA GLU B 602 " pdb=" CB GLU B 602 " ideal model delta harmonic sigma weight residual -122.60 -134.60 12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C GLU A 602 " pdb=" N GLU A 602 " pdb=" CA GLU A 602 " pdb=" CB GLU A 602 " ideal model delta harmonic sigma weight residual -122.60 -134.58 11.98 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" N GLU B 602 " pdb=" C GLU B 602 " pdb=" CA GLU B 602 " pdb=" CB GLU B 602 " ideal model delta harmonic sigma weight residual 122.80 134.63 -11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 3557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 448 0.142 - 0.284: 70 0.284 - 0.426: 10 0.426 - 0.568: 37 0.568 - 0.710: 19 Chirality restraints: 584 Sorted by residual: chirality pdb=" CG LEU A 472 " pdb=" CB LEU A 472 " pdb=" CD1 LEU A 472 " pdb=" CD2 LEU A 472 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CG LEU B 472 " pdb=" CB LEU B 472 " pdb=" CD1 LEU B 472 " pdb=" CD2 LEU B 472 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CB ILE A 608 " pdb=" CA ILE A 608 " pdb=" CG1 ILE A 608 " pdb=" CG2 ILE A 608 " both_signs ideal model delta sigma weight residual False 2.64 1.97 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 581 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 644 " 0.161 2.00e-02 2.50e+03 4.80e-01 3.45e+03 pdb=" CG ASN B 644 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 644 " -0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN B 644 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 644 " -0.813 2.00e-02 2.50e+03 pdb="HD22 ASN B 644 " 0.818 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 644 " -0.162 2.00e-02 2.50e+03 4.80e-01 3.45e+03 pdb=" CG ASN A 644 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 644 " 0.159 2.00e-02 2.50e+03 pdb=" ND2 ASN A 644 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 644 " 0.813 2.00e-02 2.50e+03 pdb="HD22 ASN A 644 " -0.818 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 455 " -0.245 2.00e-02 2.50e+03 8.72e-02 3.04e+02 pdb=" CG TRP A 455 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 455 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A 455 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP A 455 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TRP A 455 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 455 " 0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 455 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 455 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A 455 " -0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP A 455 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP A 455 " 0.103 2.00e-02 2.50e+03 pdb=" HE3 TRP A 455 " 0.120 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 455 " -0.091 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 455 " 0.060 2.00e-02 2.50e+03 pdb=" HH2 TRP A 455 " -0.081 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 1 1.35 - 2.16: 497 2.16 - 2.97: 20195 2.97 - 3.79: 34287 3.79 - 4.60: 54979 Warning: very small nonbonded interaction distances. Nonbonded interactions: 109959 Sorted by model distance: nonbonded pdb=" H2 HOH A 803 " pdb=" H2 HOH B 803 " model vdw 0.536 2.100 nonbonded pdb=" O ARG A 567 " pdb=" H2 HOH A 801 " model vdw 1.440 1.850 nonbonded pdb=" H2 HOH A 803 " pdb=" O HOH B 803 " model vdw 1.474 1.850 nonbonded pdb=" O HOH A 803 " pdb=" H2 HOH B 803 " model vdw 1.475 1.850 nonbonded pdb="HH22 ARG B 519 " pdb="HD21 ASN B 542 " model vdw 1.547 2.100 ... (remaining 109954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 31.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.023 0.132 3898 Z= 1.466 Angle : 2.286 13.446 5326 Z= 1.471 Chirality : 0.199 0.710 584 Planarity : 0.014 0.078 684 Dihedral : 15.900 89.986 1400 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.45 % Allowed : 6.76 % Favored : 91.79 % Cbeta Deviations : 5.50 % 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: -2.38 (0.35), residues: 456 helix: -2.80 (0.26), residues: 182 sheet: -0.24 (0.62), residues: 56 loop : -0.63 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.033 TRP A 455 HIS 0.009 0.005 HIS B 448 PHE 0.080 0.018 PHE B 580 TYR 0.111 0.026 TYR A 512 ARG 0.008 0.002 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 107 average time/residue: 1.8114 time to fit residues: 201.8192 Evaluate side-chains 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3898 Z= 0.221 Angle : 0.600 5.729 5326 Z= 0.313 Chirality : 0.041 0.155 584 Planarity : 0.005 0.046 684 Dihedral : 5.497 18.223 492 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.66 % Allowed : 14.01 % Favored : 83.33 % 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: -0.94 (0.37), residues: 456 helix: -0.84 (0.35), residues: 176 sheet: 0.05 (0.57), residues: 68 loop : -0.49 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 591 HIS 0.003 0.001 HIS A 613 PHE 0.011 0.002 PHE B 564 TYR 0.008 0.002 TYR A 532 ARG 0.003 0.001 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6887 (mp0) outliers start: 11 outliers final: 3 residues processed: 88 average time/residue: 2.2249 time to fit residues: 202.8590 Evaluate side-chains 80 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 571 GLN B 456 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3898 Z= 0.194 Angle : 0.536 5.607 5326 Z= 0.276 Chirality : 0.040 0.151 584 Planarity : 0.005 0.043 684 Dihedral : 4.796 14.203 492 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.66 % Allowed : 16.18 % Favored : 81.16 % 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: -0.56 (0.38), residues: 456 helix: -0.20 (0.38), residues: 176 sheet: 0.27 (0.56), residues: 68 loop : -0.60 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 591 HIS 0.005 0.002 HIS A 613 PHE 0.009 0.002 PHE A 516 TYR 0.009 0.001 TYR A 532 ARG 0.002 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ILE cc_start: 0.8143 (mp) cc_final: 0.7875 (mm) REVERT: A 601 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: B 514 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: B 567 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7516 (mtm110) outliers start: 11 outliers final: 0 residues processed: 80 average time/residue: 2.2173 time to fit residues: 183.8791 Evaluate side-chains 79 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain B residue 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3898 Z= 0.311 Angle : 0.581 5.473 5326 Z= 0.300 Chirality : 0.042 0.156 584 Planarity : 0.005 0.047 684 Dihedral : 4.917 14.953 492 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.38 % Allowed : 16.18 % Favored : 80.43 % 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: -0.68 (0.38), residues: 456 helix: -0.18 (0.38), residues: 176 sheet: 0.21 (0.57), residues: 68 loop : -0.79 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 591 HIS 0.005 0.002 HIS B 613 PHE 0.011 0.002 PHE A 516 TYR 0.014 0.002 TYR A 532 ARG 0.004 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 ILE cc_start: 0.8236 (mp) cc_final: 0.8033 (mm) REVERT: B 514 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6661 (tp30) outliers start: 14 outliers final: 5 residues processed: 82 average time/residue: 2.3028 time to fit residues: 195.2423 Evaluate side-chains 81 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3898 Z= 0.257 Angle : 0.554 5.608 5326 Z= 0.285 Chirality : 0.041 0.154 584 Planarity : 0.005 0.046 684 Dihedral : 4.769 14.105 492 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.90 % Allowed : 19.81 % Favored : 77.29 % 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: -0.65 (0.38), residues: 456 helix: -0.00 (0.39), residues: 176 sheet: 0.17 (0.57), residues: 68 loop : -0.92 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 591 HIS 0.005 0.002 HIS B 613 PHE 0.010 0.002 PHE A 516 TYR 0.011 0.002 TYR B 532 ARG 0.004 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7455 (mtm110) REVERT: B 514 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6652 (tp30) REVERT: B 567 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7506 (mtm110) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 2.3528 time to fit residues: 184.9537 Evaluate side-chains 69 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 573 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3898 Z= 0.221 Angle : 0.535 5.632 5326 Z= 0.274 Chirality : 0.040 0.154 584 Planarity : 0.005 0.045 684 Dihedral : 4.648 14.409 492 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.66 % Allowed : 19.57 % Favored : 77.78 % 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: -0.57 (0.38), residues: 456 helix: 0.14 (0.39), residues: 176 sheet: 0.15 (0.56), residues: 68 loop : -0.93 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 591 HIS 0.005 0.002 HIS A 613 PHE 0.009 0.002 PHE B 516 TYR 0.010 0.002 TYR B 532 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7475 (mtm110) REVERT: B 514 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6590 (tp30) outliers start: 11 outliers final: 4 residues processed: 74 average time/residue: 2.2205 time to fit residues: 170.3302 Evaluate side-chains 73 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3898 Z= 0.193 Angle : 0.528 5.662 5326 Z= 0.268 Chirality : 0.040 0.157 584 Planarity : 0.005 0.044 684 Dihedral : 4.487 14.168 492 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.42 % Allowed : 20.77 % Favored : 76.81 % 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: -0.42 (0.38), residues: 456 helix: 0.31 (0.39), residues: 176 sheet: 0.00 (0.56), residues: 68 loop : -0.79 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.004 0.002 HIS B 613 PHE 0.008 0.002 PHE A 516 TYR 0.009 0.001 TYR A 532 ARG 0.002 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7475 (mtm110) REVERT: B 602 GLU cc_start: 0.7042 (mp0) cc_final: 0.6579 (mt-10) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 2.2634 time to fit residues: 173.9154 Evaluate side-chains 71 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 573 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3898 Z= 0.174 Angle : 0.519 5.661 5326 Z= 0.262 Chirality : 0.039 0.158 584 Planarity : 0.005 0.042 684 Dihedral : 4.366 14.197 492 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.69 % Allowed : 21.26 % Favored : 77.05 % 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: -0.26 (0.39), residues: 456 helix: 0.53 (0.40), residues: 176 sheet: -0.01 (0.56), residues: 68 loop : -0.75 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.004 0.002 HIS A 613 PHE 0.007 0.001 PHE A 516 TYR 0.008 0.001 TYR B 532 ARG 0.002 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7481 (mtm110) outliers start: 7 outliers final: 4 residues processed: 75 average time/residue: 2.5539 time to fit residues: 198.0826 Evaluate side-chains 67 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3898 Z= 0.162 Angle : 0.521 8.489 5326 Z= 0.260 Chirality : 0.039 0.158 584 Planarity : 0.004 0.041 684 Dihedral : 4.241 13.973 492 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.69 % Allowed : 21.74 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.39), residues: 456 helix: 0.70 (0.40), residues: 176 sheet: -0.02 (0.57), residues: 68 loop : -0.67 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.004 0.001 HIS B 613 PHE 0.006 0.001 PHE A 617 TYR 0.007 0.001 TYR B 532 ARG 0.003 0.000 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 602 GLU cc_start: 0.6924 (mp0) cc_final: 0.6460 (mt-10) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 2.0482 time to fit residues: 147.1285 Evaluate side-chains 72 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 573 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3898 Z= 0.205 Angle : 0.539 7.503 5326 Z= 0.271 Chirality : 0.040 0.159 584 Planarity : 0.005 0.042 684 Dihedral : 4.323 14.516 492 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.45 % Allowed : 21.74 % Favored : 76.81 % 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: -0.15 (0.39), residues: 456 helix: 0.67 (0.40), residues: 176 sheet: -0.00 (0.57), residues: 68 loop : -0.72 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 561 HIS 0.004 0.001 HIS A 613 PHE 0.008 0.001 PHE A 516 TYR 0.010 0.001 TYR B 532 ARG 0.003 0.000 ARG B 606 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7532 (mtm110) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 2.1586 time to fit residues: 166.1292 Evaluate side-chains 72 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 573 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.189130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175111 restraints weight = 11577.274| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.71 r_work: 0.3988 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3898 Z= 0.177 Angle : 0.544 7.644 5326 Z= 0.271 Chirality : 0.039 0.157 584 Planarity : 0.005 0.042 684 Dihedral : 4.243 14.052 492 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.45 % Allowed : 22.71 % Favored : 75.85 % 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: -0.07 (0.40), residues: 456 helix: 0.77 (0.40), residues: 176 sheet: 0.02 (0.57), residues: 68 loop : -0.69 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.004 0.001 HIS A 613 PHE 0.006 0.001 PHE B 516 TYR 0.008 0.001 TYR A 532 ARG 0.002 0.000 ARG B 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.79 seconds wall clock time: 78 minutes 41.76 seconds (4721.76 seconds total)