Starting phenix.real_space_refine on Fri Dec 8 06:49:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/12_2023/8qa4_18298_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/12_2023/8qa4_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_18298/12_2023/8qa4_18298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/12_2023/8qa4_18298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/12_2023/8qa4_18298_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa4_18298/12_2023/8qa4_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.03, 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: 6.32 Conformation dependent library (CDL) restraints added in 735.2 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: 2.42 Time building geometry restraints manager: 6.53 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: 3120 18.00 - 35.99: 182 35.99 - 53.99: 73 53.99 - 71.99: 47 71.99 - 89.99: 10 Dihedral angle restraints: 3432 sinusoidal: 1798 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 3429 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: 3.330 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: 13.620 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.150 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.430 ------------------------------------------------------------------------------- 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 : 0.622 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: 1.8993 time to fit residues: 213.9751 Evaluate side-chains 75 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7588 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 571 GLN B 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3898 Z= 0.236 Angle : 0.591 5.811 5326 Z= 0.307 Chirality : 0.041 0.145 584 Planarity : 0.005 0.048 684 Dihedral : 5.496 15.896 492 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 14.01 % Favored : 83.82 % 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: -1.59 (0.36), residues: 456 helix: -1.80 (0.32), residues: 182 sheet: 0.07 (0.56), residues: 68 loop : -0.53 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 455 HIS 0.003 0.001 HIS A 613 PHE 0.009 0.002 PHE B 564 TYR 0.009 0.002 TYR B 532 ARG 0.004 0.001 ARG A 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 : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 90 average time/residue: 2.2050 time to fit residues: 205.4551 Evaluate side-chains 77 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 3.2744 time to fit residues: 4.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3446 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= 0.207 Angle : 0.543 5.459 5326 Z= 0.279 Chirality : 0.041 0.140 584 Planarity : 0.005 0.049 684 Dihedral : 4.934 15.007 492 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.45 % Allowed : 17.63 % Favored : 80.92 % 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: -1.17 (0.38), residues: 456 helix: -1.28 (0.35), residues: 180 sheet: 0.29 (0.57), residues: 68 loop : -0.49 (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 0.011 0.002 PHE A 508 TYR 0.009 0.002 TYR B 532 ARG 0.002 0.000 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 87 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.596 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 82 average time/residue: 2.1681 time to fit residues: 184.4671 Evaluate side-chains 80 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.3698 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= 0.211 Angle : 0.533 5.638 5326 Z= 0.272 Chirality : 0.040 0.135 584 Planarity : 0.005 0.050 684 Dihedral : 4.667 14.303 492 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.69 % Allowed : 19.57 % 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: -0.95 (0.38), residues: 456 helix: -0.99 (0.37), residues: 180 sheet: 0.33 (0.54), residues: 68 loop : -0.45 (0.45), 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 0.002 TYR B 538 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 87 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.651 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 2.1246 time to fit residues: 178.5971 Evaluate side-chains 81 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1182 time to fit residues: 1.3030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 1.9990 chunk 11 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3898 Z= 0.280 Angle : 0.565 5.526 5326 Z= 0.289 Chirality : 0.042 0.146 584 Planarity : 0.005 0.051 684 Dihedral : 4.789 14.646 492 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.42 % Allowed : 20.05 % Favored : 77.54 % 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 (0.39), residues: 456 helix: -0.86 (0.38), residues: 178 sheet: 0.33 (0.56), residues: 68 loop : -0.57 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS B 613 PHE 0.010 0.002 PHE B 516 TYR 0.012 0.002 TYR B 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 86 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.543 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 78 average time/residue: 2.1460 time to fit residues: 173.6244 Evaluate side-chains 77 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0866 time to fit residues: 0.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.4091 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= 0.340 Angle : 0.599 5.523 5326 Z= 0.308 Chirality : 0.043 0.152 584 Planarity : 0.005 0.050 684 Dihedral : 5.009 14.809 492 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.38 % Allowed : 18.84 % 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: -1.22 (0.39), residues: 456 helix: -0.98 (0.38), residues: 180 sheet: 0.21 (0.58), residues: 68 loop : -0.86 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 583 HIS 0.003 0.001 HIS B 613 PHE 0.011 0.002 PHE B 516 TYR 0.014 0.002 TYR B 532 ARG 0.005 0.001 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 89 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.624 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 83 average time/residue: 2.1300 time to fit residues: 183.5680 Evaluate side-chains 74 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.5816 time to fit residues: 2.6956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.7828 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3898 Z= 0.160 Angle : 0.522 5.661 5326 Z= 0.265 Chirality : 0.040 0.138 584 Planarity : 0.005 0.047 684 Dihedral : 4.570 13.697 492 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: -0.81 (0.39), residues: 456 helix: -0.54 (0.40), residues: 178 sheet: 0.01 (0.54), residues: 68 loop : -0.57 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 561 HIS 0.003 0.001 HIS A 539 PHE 0.011 0.001 PHE B 508 TYR 0.007 0.001 TYR A 538 ARG 0.002 0.000 ARG B 476 *********************** 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 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.601 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 76 average time/residue: 2.0891 time to fit residues: 165.0079 Evaluate side-chains 74 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.4163 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= 0.221 Angle : 0.543 5.640 5326 Z= 0.275 Chirality : 0.041 0.141 584 Planarity : 0.005 0.048 684 Dihedral : 4.610 14.696 492 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.72 % Allowed : 23.19 % Favored : 76.09 % 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: -0.78 (0.40), residues: 456 helix: -0.49 (0.40), residues: 178 sheet: 0.07 (0.56), residues: 68 loop : -0.59 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.002 0.001 HIS A 613 PHE 0.008 0.002 PHE B 508 TYR 0.010 0.001 TYR B 532 ARG 0.006 0.001 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 78 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.603 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 78 average time/residue: 2.0696 time to fit residues: 167.7634 Evaluate side-chains 70 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3898 Z= 0.172 Angle : 0.524 5.674 5326 Z= 0.266 Chirality : 0.039 0.136 584 Planarity : 0.005 0.046 684 Dihedral : 4.399 13.987 492 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.97 % Allowed : 23.19 % 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: -0.65 (0.40), residues: 456 helix: -0.39 (0.40), residues: 180 sheet: 0.01 (0.55), residues: 68 loop : -0.45 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 561 HIS 0.002 0.001 HIS B 613 PHE 0.009 0.001 PHE B 508 TYR 0.008 0.001 TYR B 538 ARG 0.006 0.001 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 75 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.623 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 2.0239 time to fit residues: 154.2062 Evaluate side-chains 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0860 time to fit residues: 1.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4310 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= 0.236 Angle : 0.557 5.677 5326 Z= 0.283 Chirality : 0.041 0.140 584 Planarity : 0.005 0.048 684 Dihedral : 4.515 14.620 492 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.72 % Allowed : 23.67 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.39), residues: 456 helix: -0.40 (0.40), residues: 178 sheet: 0.06 (0.55), residues: 68 loop : -0.55 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 583 HIS 0.003 0.001 HIS A 613 PHE 0.009 0.002 PHE A 516 TYR 0.010 0.002 TYR A 532 ARG 0.006 0.001 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 81 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.592 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 1.8717 time to fit residues: 157.5196 Evaluate side-chains 76 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.0070 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.188731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173813 restraints weight = 11444.367| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.69 r_work: 0.3981 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4427 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= 0.176 Angle : 0.539 5.692 5326 Z= 0.273 Chirality : 0.040 0.135 584 Planarity : 0.005 0.046 684 Dihedral : 4.326 14.251 492 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.24 % Allowed : 24.64 % 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: -0.59 (0.40), residues: 456 helix: -0.22 (0.40), residues: 178 sheet: -0.05 (0.54), residues: 68 loop : -0.50 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 561 HIS 0.002 0.001 HIS A 613 PHE 0.009 0.001 PHE B 508 TYR 0.008 0.001 TYR A 538 ARG 0.006 0.000 ARG A 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.96 seconds wall clock time: 78 minutes 55.10 seconds (4735.10 seconds total)