Starting phenix.real_space_refine on Sat Apr 6 07:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/04_2024/8qa4_18298_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/04_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_18298/04_2024/8qa4_18298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/04_2024/8qa4_18298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/04_2024/8qa4_18298_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/04_2024/8qa4_18298_trim_updated.pdb" } 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 3686 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7506 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 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: 4.08, per 1000 atoms: 0.54 Number of scatterers: 7506 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 3686 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: 6.94 Conformation dependent library (CDL) restraints added in 795.7 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... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 38.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 462 through 477 removed outlier: 4.071A pdb=" N LYS A 468 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 470 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 removed outlier: 3.801A pdb=" N LYS A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 579 through 594 removed outlier: 4.209A pdb=" N LYS A 584 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE A 588 " --> pdb=" O ASP A 585 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 590 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 594 " --> pdb=" O TRP A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 462 through 477 removed outlier: 4.070A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU B 469 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 470 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 removed outlier: 3.802A pdb=" N LYS B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 579 through 594 removed outlier: 4.208A pdb=" N LYS B 584 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 588 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 590 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 594 " --> pdb=" O TRP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 632 through 643 Processing sheet with id= A, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.953A pdb=" N THR A 573 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 541 removed outlier: 3.726A pdb=" N ALA A 511 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 516 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N THR A 481 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 506 through 509 removed outlier: 6.953A pdb=" N THR B 573 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 536 through 541 removed outlier: 3.726A pdb=" N ALA B 511 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 516 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N THR B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 318 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: 2.60 Time building geometry restraints manager: 7.02 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: 830 1.05 - 1.24: 3378 1.24 - 1.43: 1290 1.43 - 1.62: 2070 1.62 - 1.81: 16 Bond restraints: 7584 Sorted by residual: 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=" CE2 TYR B 438 " pdb=" HE2 TYR B 438 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLU A 553 " pdb=" H GLU A 553 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE1 TYR B 506 " pdb=" HE1 TYR B 506 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ASN B 456 " pdb=" H ASN B 456 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 7579 not shown) Histogram of bond angle deviations from ideal: 97.15 - 105.01: 349 105.01 - 112.88: 8051 112.88 - 120.74: 3651 120.74 - 128.61: 1505 128.61 - 136.47: 80 Bond angle restraints: 13636 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 13631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3192 18.00 - 35.99: 192 35.99 - 53.99: 91 53.99 - 71.99: 49 71.99 - 89.99: 10 Dihedral angle restraints: 3534 sinusoidal: 1900 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 3531 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: 1114 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 1111 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 1 1.35 - 2.16: 521 2.16 - 2.97: 20006 2.97 - 3.79: 33983 3.79 - 4.60: 54485 Warning: very small nonbonded interaction distances. Nonbonded interactions: 108996 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 108991 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: 3.660 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: 0.110 Extract box with map and model: 14.000 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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= 1.476 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 108 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 108 average time/residue: 1.8680 time to fit residues: 210.1742 Evaluate side-chains 75 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 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 456 ASN A 571 GLN B 456 ASN B 542 ASN B 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3898 Z= 0.251 Angle : 0.601 5.723 5326 Z= 0.313 Chirality : 0.042 0.144 584 Planarity : 0.005 0.047 684 Dihedral : 5.591 16.778 492 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.17 % Allowed : 14.73 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.36), residues: 456 helix: -1.83 (0.33), residues: 182 sheet: 0.03 (0.56), residues: 68 loop : -0.57 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 455 HIS 0.002 0.001 HIS A 613 PHE 0.011 0.002 PHE B 564 TYR 0.009 0.002 TYR B 538 ARG 0.004 0.001 ARG B 476 *********************** 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: 9 poor density : 88 time to evaluate : 0.556 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 90 average time/residue: 2.2475 time to fit residues: 209.3712 Evaluate side-chains 79 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 473 ARG 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: 0.9980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 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 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3486 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= 0.200 Angle : 0.540 5.393 5326 Z= 0.277 Chirality : 0.041 0.140 584 Planarity : 0.005 0.048 684 Dihedral : 4.906 14.473 492 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.93 % Allowed : 16.67 % Favored : 81.40 % 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: -1.20 (0.38), residues: 456 helix: -1.27 (0.36), residues: 180 sheet: 0.33 (0.57), residues: 68 loop : -0.57 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 583 HIS 0.003 0.001 HIS B 613 PHE 0.011 0.002 PHE A 508 TYR 0.009 0.002 TYR A 532 ARG 0.002 0.001 ARG A 476 *********************** 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 91 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.619 Fit side-chains REVERT: B 514 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: B 567 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7534 (mtm110) outliers start: 8 outliers final: 0 residues processed: 84 average time/residue: 2.1973 time to fit residues: 191.4704 Evaluate side-chains 82 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.3679 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= 0.218 Angle : 0.535 5.559 5326 Z= 0.273 Chirality : 0.041 0.137 584 Planarity : 0.005 0.049 684 Dihedral : 4.712 14.185 492 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.45 % Allowed : 19.81 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.38), residues: 456 helix: -1.05 (0.37), residues: 180 sheet: 0.29 (0.54), residues: 68 loop : -0.54 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 583 HIS 0.002 0.001 HIS B 613 PHE 0.009 0.002 PHE A 508 TYR 0.010 0.001 TYR A 532 ARG 0.003 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 87 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.638 Fit side-chains REVERT: B 514 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6661 (tp30) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 2.0544 time to fit residues: 175.0257 Evaluate side-chains 81 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 534 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3898 Z= 0.376 Angle : 0.623 5.468 5326 Z= 0.320 Chirality : 0.044 0.154 584 Planarity : 0.005 0.052 684 Dihedral : 5.122 15.598 492 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.11 % Allowed : 17.87 % Favored : 78.02 % 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: -1.24 (0.38), residues: 456 helix: -1.12 (0.38), residues: 178 sheet: 0.27 (0.58), residues: 68 loop : -0.77 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 583 HIS 0.003 0.001 HIS B 613 PHE 0.012 0.002 PHE B 626 TYR 0.016 0.002 TYR A 532 ARG 0.004 0.001 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 93 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.597 Fit side-chains REVERT: A 570 ILE cc_start: 0.8241 (mt) cc_final: 0.7960 (mm) outliers start: 17 outliers final: 4 residues processed: 80 average time/residue: 2.1750 time to fit residues: 180.4765 Evaluate side-chains 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR 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: 0.7980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3898 Z= 0.197 Angle : 0.536 5.631 5326 Z= 0.273 Chirality : 0.040 0.141 584 Planarity : 0.005 0.046 684 Dihedral : 4.748 13.833 492 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 20.77 % 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: -1.04 (0.39), residues: 456 helix: -0.81 (0.39), residues: 178 sheet: 0.10 (0.55), residues: 68 loop : -0.69 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.002 0.001 HIS B 613 PHE 0.009 0.002 PHE B 508 TYR 0.009 0.001 TYR A 532 ARG 0.004 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 83 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.662 Fit side-chains REVERT: A 428 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 567 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7485 (mtm110) REVERT: A 570 ILE cc_start: 0.8261 (mt) cc_final: 0.8005 (mm) REVERT: A 581 MET cc_start: 0.7193 (mmm) cc_final: 0.6967 (mmm) REVERT: B 428 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 567 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7487 (mtm110) outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 2.2156 time to fit residues: 183.8403 Evaluate side-chains 79 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 428 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: 0.9980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3898 Z= 0.177 Angle : 0.519 5.671 5326 Z= 0.262 Chirality : 0.040 0.139 584 Planarity : 0.005 0.046 684 Dihedral : 4.509 14.024 492 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -0.85 (0.39), residues: 456 helix: -0.61 (0.39), residues: 180 sheet: -0.02 (0.55), residues: 68 loop : -0.55 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 561 HIS 0.002 0.001 HIS B 539 PHE 0.009 0.001 PHE B 508 TYR 0.008 0.001 TYR A 532 ARG 0.003 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 84 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.570 Fit side-chains REVERT: A 567 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7508 (mtm110) REVERT: A 570 ILE cc_start: 0.8252 (mt) cc_final: 0.8002 (mm) REVERT: B 567 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7514 (mtm110) outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 2.0241 time to fit residues: 174.9299 Evaluate side-chains 72 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3898 Z= 0.189 Angle : 0.526 5.689 5326 Z= 0.266 Chirality : 0.040 0.137 584 Planarity : 0.005 0.045 684 Dihedral : 4.458 14.107 492 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.97 % Allowed : 23.67 % Favored : 75.36 % 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: -0.73 (0.39), residues: 456 helix: -0.47 (0.39), residues: 180 sheet: 0.03 (0.55), residues: 68 loop : -0.51 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 561 HIS 0.002 0.001 HIS A 613 PHE 0.009 0.001 PHE B 508 TYR 0.009 0.001 TYR A 532 ARG 0.003 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 77 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.610 Fit side-chains REVERT: A 567 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7532 (mtm110) REVERT: A 570 ILE cc_start: 0.8267 (mt) cc_final: 0.8013 (mm) REVERT: B 567 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7529 (mtm110) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 2.0290 time to fit residues: 156.3658 Evaluate side-chains 77 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR 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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4266 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= 0.174 Angle : 0.521 5.679 5326 Z= 0.263 Chirality : 0.040 0.135 584 Planarity : 0.005 0.045 684 Dihedral : 4.334 13.961 492 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.97 % Allowed : 23.91 % Favored : 75.12 % 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 (0.39), residues: 456 helix: -0.29 (0.40), residues: 180 sheet: 0.03 (0.55), residues: 68 loop : -0.44 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.002 0.001 HIS A 613 PHE 0.009 0.001 PHE B 508 TYR 0.008 0.001 TYR A 532 ARG 0.003 0.000 ARG A 567 *********************** 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 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.620 Fit side-chains REVERT: A 567 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7541 (mtm110) REVERT: A 570 ILE cc_start: 0.8264 (mt) cc_final: 0.8012 (mm) REVERT: B 514 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: B 567 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7543 (mtm110) outliers start: 4 outliers final: 0 residues processed: 77 average time/residue: 2.0622 time to fit residues: 165.0782 Evaluate side-chains 74 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 GLU 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: 0.0030 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7472 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.4312 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= 0.197 Angle : 0.544 7.596 5326 Z= 0.273 Chirality : 0.040 0.136 584 Planarity : 0.005 0.045 684 Dihedral : 4.394 14.174 492 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.72 % Allowed : 24.40 % Favored : 74.88 % 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: -0.52 (0.39), residues: 456 helix: -0.24 (0.40), residues: 180 sheet: 0.06 (0.56), residues: 68 loop : -0.42 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 561 HIS 0.002 0.001 HIS A 613 PHE 0.008 0.001 PHE B 508 TYR 0.009 0.001 TYR A 532 ARG 0.002 0.000 ARG A 567 ********************** 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 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.635 Fit side-chains REVERT: A 567 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7545 (mtm110) REVERT: A 570 ILE cc_start: 0.8275 (mt) cc_final: 0.8027 (mm) REVERT: B 514 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: B 567 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7539 (mtm110) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 2.0447 time to fit residues: 163.7347 Evaluate side-chains 79 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.0010 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.188408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173559 restraints weight = 11511.097| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.70 r_work: 0.3976 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4334 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= 0.170 Angle : 0.529 6.927 5326 Z= 0.265 Chirality : 0.040 0.135 584 Planarity : 0.005 0.044 684 Dihedral : 4.283 13.898 492 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.21 % Allowed : 23.91 % Favored : 74.88 % 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 (0.40), residues: 456 helix: -0.14 (0.40), residues: 180 sheet: 0.02 (0.56), residues: 68 loop : -0.35 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.002 0.001 HIS A 613 PHE 0.008 0.001 PHE B 508 TYR 0.007 0.001 TYR A 532 ARG 0.002 0.000 ARG A 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4507.81 seconds wall clock time: 79 minutes 52.36 seconds (4792.36 seconds total)