Starting phenix.real_space_refine on Mon Mar 11 00:43:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/03_2024/7s1z_24813.pdb" } resolution = 3.3 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= 0.010 sd= 0.150 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4224 2.51 5 N 1034 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3208 Classifications: {'peptide': 472} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 456} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 208 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3208 Classifications: {'peptide': 472} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 456} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 208 Time building chain proxies: 4.26, per 1000 atoms: 0.66 Number of scatterers: 6416 At special positions: 0 Unit cell: (104.94, 83.74, 87.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1124 8.00 N 1034 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.532A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.532A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 4.115A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 398 removed outlier: 4.508A pdb=" N GLY A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.502A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 454 removed outlier: 3.650A pdb=" N ALA A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.651A pdb=" N LYS A 460 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 461' Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.358A pdb=" N GLY A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 516 through 542 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.599A pdb=" N CYS A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 570 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.562A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 630 removed outlier: 3.647A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 654 through 667 removed outlier: 4.131A pdb=" N THR A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 699 removed outlier: 4.242A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 730 Processing helix chain 'A' and resid 731 through 753 Processing helix chain 'B' and resid 288 through 300 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.441A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.511A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 344 removed outlier: 4.170A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 398 removed outlier: 4.482A pdb=" N GLY B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.654A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 removed outlier: 3.639A pdb=" N ALA B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.646A pdb=" N LYS B 460 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 461' Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 5.936A pdb=" N GLY B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.585A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 516 through 542 Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.598A pdb=" N CYS B 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 570 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.529A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 630 removed outlier: 3.526A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.964A pdb=" N THR B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 699 removed outlier: 3.924A pdb=" N ILE B 677 " --> pdb=" O VAL B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.505A pdb=" N SER B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 753 473 hydrogen bonds defined for protein. 1395 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: 1.71 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2004 1.34 - 1.46: 1560 1.46 - 1.58: 2948 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 6560 Sorted by residual: bond pdb=" CG1 ILE B 747 " pdb=" CD1 ILE B 747 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG1 ILE A 747 " pdb=" CD1 ILE A 747 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.22e+00 bond pdb=" C ALA B 675 " pdb=" N PRO B 676 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.91e+00 bond pdb=" C ALA A 675 " pdb=" N PRO A 676 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.76e+00 bond pdb=" C PHE A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.44e-02 4.82e+03 1.59e+00 ... (remaining 6555 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.51: 139 106.51 - 113.41: 3610 113.41 - 120.31: 2428 120.31 - 127.21: 2749 127.21 - 134.11: 54 Bond angle restraints: 8980 Sorted by residual: angle pdb=" N ILE A 507 " pdb=" CA ILE A 507 " pdb=" C ILE A 507 " ideal model delta sigma weight residual 112.80 106.16 6.64 1.15e+00 7.56e-01 3.33e+01 angle pdb=" N ILE B 507 " pdb=" CA ILE B 507 " pdb=" C ILE B 507 " ideal model delta sigma weight residual 113.07 107.03 6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" N ILE B 556 " pdb=" CA ILE B 556 " pdb=" C ILE B 556 " ideal model delta sigma weight residual 111.91 108.72 3.19 8.90e-01 1.26e+00 1.28e+01 angle pdb=" N ILE A 556 " pdb=" CA ILE A 556 " pdb=" C ILE A 556 " ideal model delta sigma weight residual 111.91 108.85 3.06 8.90e-01 1.26e+00 1.18e+01 angle pdb=" N SER A 516 " pdb=" CA SER A 516 " pdb=" C SER A 516 " ideal model delta sigma weight residual 112.72 109.19 3.53 1.28e+00 6.10e-01 7.60e+00 ... (remaining 8975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 3350 16.22 - 32.45: 255 32.45 - 48.67: 50 48.67 - 64.89: 3 64.89 - 81.12: 4 Dihedral angle restraints: 3662 sinusoidal: 1056 harmonic: 2606 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.59 71.41 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.64 71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA GLY A 286 " pdb=" C GLY A 286 " pdb=" N TRP A 287 " pdb=" CA TRP A 287 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 309 0.052 - 0.079: 162 0.079 - 0.105: 58 0.105 - 0.131: 10 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CG LEU B 743 " pdb=" CB LEU B 743 " pdb=" CD1 LEU B 743 " pdb=" CD2 LEU B 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CG LEU A 743 " pdb=" CB LEU A 743 " pdb=" CD1 LEU A 743 " pdb=" CD2 LEU A 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 507 " pdb=" N ILE B 507 " pdb=" C ILE B 507 " pdb=" CB ILE B 507 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1091 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 705 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO B 706 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 675 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 676 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 675 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 676 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.046 5.00e-02 4.00e+02 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1424 2.78 - 3.31: 6932 3.31 - 3.84: 10887 3.84 - 4.37: 11091 4.37 - 4.90: 19946 Nonbonded interactions: 50280 Sorted by model distance: nonbonded pdb=" OD1 ASN A 476 " pdb=" NH1 ARG A 546 " model vdw 2.245 2.520 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 692 " model vdw 2.260 2.440 nonbonded pdb=" O ILE A 356 " pdb=" OG SER A 692 " model vdw 2.274 2.440 nonbonded pdb=" O VAL B 450 " pdb=" OG1 THR B 453 " model vdw 2.299 2.440 nonbonded pdb=" O VAL A 450 " pdb=" OG1 THR A 453 " model vdw 2.305 2.440 ... (remaining 50275 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.360 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6560 Z= 0.217 Angle : 0.702 7.266 8980 Z= 0.397 Chirality : 0.041 0.131 1094 Planarity : 0.007 0.098 1126 Dihedral : 12.332 81.117 2010 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % 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: -0.47 (0.27), residues: 940 helix: 1.26 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.30 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 300 HIS 0.005 0.001 HIS B 695 PHE 0.021 0.001 PHE B 364 TYR 0.011 0.001 TYR A 533 ARG 0.008 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.684 Fit side-chains REVERT: A 428 MET cc_start: 0.4302 (tpp) cc_final: 0.3394 (ttp) REVERT: A 469 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6396 (mmtt) REVERT: A 713 MET cc_start: 0.5462 (ptp) cc_final: 0.5207 (ptm) REVERT: B 428 MET cc_start: 0.4384 (tpp) cc_final: 0.3450 (ttp) REVERT: B 469 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6809 (mmtp) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1440 time to fit residues: 12.5829 Evaluate side-chains 45 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6560 Z= 0.198 Angle : 0.584 5.161 8980 Z= 0.303 Chirality : 0.041 0.127 1094 Planarity : 0.006 0.073 1126 Dihedral : 4.515 23.652 974 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.71 % Allowed : 9.43 % Favored : 89.86 % 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: -0.20 (0.28), residues: 940 helix: 1.42 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.26 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 732 HIS 0.002 0.000 HIS B 695 PHE 0.015 0.002 PHE B 681 TYR 0.006 0.001 TYR A 533 ARG 0.003 0.001 ARG B 705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.622 Fit side-chains REVERT: A 428 MET cc_start: 0.4300 (tpp) cc_final: 0.3453 (ttp) REVERT: A 469 LYS cc_start: 0.6792 (mmmt) cc_final: 0.6477 (mmtp) REVERT: B 428 MET cc_start: 0.4433 (tpp) cc_final: 0.3559 (ttp) outliers start: 4 outliers final: 0 residues processed: 53 average time/residue: 0.1452 time to fit residues: 11.7508 Evaluate side-chains 41 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6560 Z= 0.267 Angle : 0.601 5.243 8980 Z= 0.316 Chirality : 0.043 0.125 1094 Planarity : 0.005 0.067 1126 Dihedral : 4.601 22.387 974 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.42 % Allowed : 14.77 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 940 helix: 1.29 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.40 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 714 HIS 0.001 0.001 HIS A 398 PHE 0.017 0.002 PHE B 364 TYR 0.008 0.001 TYR A 584 ARG 0.003 0.001 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.636 Fit side-chains REVERT: A 428 MET cc_start: 0.4869 (tpp) cc_final: 0.3845 (ttp) REVERT: A 506 ASN cc_start: 0.5792 (OUTLIER) cc_final: 0.5564 (p0) REVERT: B 428 MET cc_start: 0.4931 (tpp) cc_final: 0.3947 (ttp) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 0.1384 time to fit residues: 12.3501 Evaluate side-chains 50 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 506 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.0010 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 506 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6560 Z= 0.202 Angle : 0.558 5.714 8980 Z= 0.290 Chirality : 0.041 0.138 1094 Planarity : 0.005 0.060 1126 Dihedral : 4.431 21.422 974 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 1.78 % Allowed : 17.79 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 940 helix: 1.42 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.001 0.000 HIS A 695 PHE 0.008 0.001 PHE B 364 TYR 0.005 0.001 TYR A 584 ARG 0.002 0.001 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.680 Fit side-chains REVERT: A 428 MET cc_start: 0.4814 (tpp) cc_final: 0.3875 (ttp) REVERT: B 428 MET cc_start: 0.4827 (tpp) cc_final: 0.3864 (ttp) outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.1274 time to fit residues: 10.5790 Evaluate side-chains 44 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 30 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4797 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6560 Z= 0.203 Angle : 0.551 5.541 8980 Z= 0.287 Chirality : 0.041 0.122 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.317 20.141 974 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.31 % Allowed : 18.51 % Favored : 79.18 % 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: -0.05 (0.28), residues: 940 helix: 1.64 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -3.27 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 714 HIS 0.001 0.000 HIS A 695 PHE 0.010 0.001 PHE A 728 TYR 0.005 0.001 TYR B 655 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.673 Fit side-chains REVERT: A 428 MET cc_start: 0.5013 (tpp) cc_final: 0.4133 (ttm) REVERT: A 468 TYR cc_start: 0.4241 (OUTLIER) cc_final: 0.3525 (m-10) REVERT: B 428 MET cc_start: 0.4760 (tpp) cc_final: 0.3878 (ttm) REVERT: B 499 THR cc_start: 0.7284 (p) cc_final: 0.7011 (p) outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.1305 time to fit residues: 12.0405 Evaluate side-chains 52 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4801 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6560 Z= 0.210 Angle : 0.566 6.782 8980 Z= 0.289 Chirality : 0.041 0.122 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.306 19.634 974 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.85 % Allowed : 19.57 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 940 helix: 1.66 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -3.26 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 714 HIS 0.001 0.000 HIS A 695 PHE 0.009 0.001 PHE A 728 TYR 0.007 0.001 TYR B 739 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 1.013 Fit side-chains REVERT: B 468 TYR cc_start: 0.4219 (OUTLIER) cc_final: 0.3724 (m-10) REVERT: B 499 THR cc_start: 0.7305 (p) cc_final: 0.7029 (p) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.1350 time to fit residues: 12.2533 Evaluate side-chains 52 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 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 506 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4804 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6560 Z= 0.200 Angle : 0.561 6.231 8980 Z= 0.286 Chirality : 0.041 0.122 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.263 18.982 974 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.85 % Allowed : 20.28 % Favored : 76.87 % 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: 0.05 (0.28), residues: 940 helix: 1.66 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.21 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 733 HIS 0.001 0.000 HIS A 695 PHE 0.008 0.001 PHE B 728 TYR 0.008 0.001 TYR A 739 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.626 Fit side-chains REVERT: A 468 TYR cc_start: 0.4390 (OUTLIER) cc_final: 0.3604 (m-10) REVERT: B 468 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3739 (m-10) REVERT: B 499 THR cc_start: 0.7321 (p) cc_final: 0.7036 (p) outliers start: 16 outliers final: 11 residues processed: 58 average time/residue: 0.1332 time to fit residues: 11.8338 Evaluate side-chains 55 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 506 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4884 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6560 Z= 0.349 Angle : 0.651 5.962 8980 Z= 0.340 Chirality : 0.045 0.177 1094 Planarity : 0.005 0.059 1126 Dihedral : 4.598 17.367 974 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.31 % Allowed : 21.89 % Favored : 75.80 % 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: -0.46 (0.28), residues: 940 helix: 1.29 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -3.32 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 714 HIS 0.002 0.001 HIS A 695 PHE 0.012 0.002 PHE B 488 TYR 0.010 0.001 TYR B 584 ARG 0.004 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.839 Fit side-chains REVERT: A 499 THR cc_start: 0.7353 (p) cc_final: 0.7101 (p) REVERT: B 499 THR cc_start: 0.7233 (p) cc_final: 0.6961 (p) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.1435 time to fit residues: 12.7576 Evaluate side-chains 53 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6560 Z= 0.225 Angle : 0.586 5.675 8980 Z= 0.301 Chirality : 0.041 0.156 1094 Planarity : 0.004 0.055 1126 Dihedral : 4.430 17.774 974 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.78 % Allowed : 22.95 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.28), residues: 940 helix: 1.50 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.26 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.001 0.000 HIS A 695 PHE 0.009 0.001 PHE B 488 TYR 0.006 0.001 TYR B 584 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.712 Fit side-chains REVERT: A 499 THR cc_start: 0.7180 (p) cc_final: 0.6919 (p) REVERT: B 499 THR cc_start: 0.7101 (p) cc_final: 0.6818 (p) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.1331 time to fit residues: 10.8705 Evaluate side-chains 51 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 0.0020 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6560 Z= 0.189 Angle : 0.564 5.651 8980 Z= 0.286 Chirality : 0.040 0.137 1094 Planarity : 0.004 0.054 1126 Dihedral : 4.233 16.962 974 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.60 % Allowed : 23.31 % Favored : 75.09 % 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: 0.05 (0.28), residues: 940 helix: 1.69 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.28 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.000 0.000 HIS A 695 PHE 0.008 0.001 PHE A 481 TYR 0.004 0.001 TYR B 584 ARG 0.001 0.000 ARG B 705 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.674 Fit side-chains REVERT: A 499 THR cc_start: 0.7056 (p) cc_final: 0.6787 (p) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.1380 time to fit residues: 10.0108 Evaluate side-chains 48 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.199014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157354 restraints weight = 6962.477| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.55 r_work: 0.3774 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 6560 Z= 0.277 Angle : 1.005 59.200 8980 Z= 0.594 Chirality : 0.054 1.171 1094 Planarity : 0.004 0.054 1126 Dihedral : 4.308 27.210 974 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.11 % Favored : 89.79 % Rotamer: Outliers : 1.60 % Allowed : 23.31 % Favored : 75.09 % Cbeta Deviations : 0.12 % 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: 0.06 (0.28), residues: 940 helix: 1.70 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.29 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 732 HIS 0.000 0.000 HIS A 695 PHE 0.007 0.001 PHE B 488 TYR 0.058 0.001 TYR A 739 ARG 0.001 0.000 ARG B 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.71 seconds wall clock time: 28 minutes 20.49 seconds (1700.49 seconds total)