Starting phenix.real_space_refine on Fri Dec 8 01:08:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/12_2023/7s1z_24813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/12_2023/7s1z_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_24813/12_2023/7s1z_24813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/12_2023/7s1z_24813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/12_2023/7s1z_24813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1z_24813/12_2023/7s1z_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-1.21rc1-5172/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: 4.24, 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: 2.82 Conformation dependent library (CDL) restraints added in 1.8 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: 0.69 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: 1.99 Time building geometry restraints manager: 3.01 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: 1.190 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: 3.870 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.480 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- 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 : 0.709 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1400 time to fit residues: 12.5900 Evaluate side-chains 43 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9531 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.4711 moved from start: 0.1099 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= 0.194 Angle : 0.580 5.097 8980 Z= 0.302 Chirality : 0.041 0.121 1094 Planarity : 0.006 0.072 1126 Dihedral : 4.474 22.912 974 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.71 % Allowed : 8.90 % Favored : 90.39 % 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: 1.46 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.29 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 732 HIS 0.001 0.000 HIS B 695 PHE 0.013 0.002 PHE B 364 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 52 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.745 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.1193 time to fit residues: 9.9871 Evaluate side-chains 41 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9130 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4781 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6560 Z= 0.233 Angle : 0.576 5.124 8980 Z= 0.302 Chirality : 0.042 0.124 1094 Planarity : 0.005 0.064 1126 Dihedral : 4.513 22.304 974 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.42 % Allowed : 14.06 % Favored : 84.52 % 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: -0.24 (0.28), residues: 940 helix: 1.37 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.001 HIS A 695 PHE 0.014 0.002 PHE B 364 TYR 0.006 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 56 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.667 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 55 average time/residue: 0.1268 time to fit residues: 10.9798 Evaluate side-chains 46 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0615 time to fit residues: 1.2213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6560 Z= 0.233 Angle : 0.564 5.296 8980 Z= 0.296 Chirality : 0.042 0.136 1094 Planarity : 0.005 0.060 1126 Dihedral : 4.444 20.826 974 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.07 % Allowed : 17.44 % Favored : 81.49 % 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: -0.29 (0.28), residues: 940 helix: 1.43 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.43 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.001 0.000 HIS A 695 PHE 0.016 0.002 PHE B 364 TYR 0.006 0.001 TYR A 584 ARG 0.002 0.000 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: 6 poor density : 47 time to evaluate : 0.693 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.1426 time to fit residues: 11.6810 Evaluate side-chains 48 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0646 time to fit residues: 1.3072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4794 moved from start: 0.2522 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= 0.206 Angle : 0.555 5.378 8980 Z= 0.290 Chirality : 0.041 0.119 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.330 19.681 974 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.31 % Allowed : 17.97 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 940 helix: 1.62 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.25 (0.31), residues: 348 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 0.011 0.001 PHE A 364 TYR 0.005 0.001 TYR A 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 58 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.680 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 58 average time/residue: 0.1368 time to fit residues: 12.2138 Evaluate side-chains 49 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0647 time to fit residues: 1.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4817 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6560 Z= 0.237 Angle : 0.582 7.132 8980 Z= 0.299 Chirality : 0.042 0.121 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.374 18.923 974 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.60 % Allowed : 19.40 % Favored : 79.00 % 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: -0.16 (0.28), residues: 940 helix: 1.55 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.28 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.001 0.000 HIS A 398 PHE 0.010 0.001 PHE B 728 TYR 0.008 0.001 TYR A 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 55 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.724 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 55 average time/residue: 0.1378 time to fit residues: 11.8251 Evaluate side-chains 48 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0649 time to fit residues: 1.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 30.0000 chunk 54 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4797 moved from start: 0.2860 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= 0.192 Angle : 0.560 6.035 8980 Z= 0.286 Chirality : 0.040 0.114 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.275 18.762 974 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.53 % Allowed : 22.24 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 940 helix: 1.61 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.19 (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 0.009 0.001 PHE B 728 TYR 0.009 0.001 TYR A 739 ARG 0.001 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 44 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.726 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1486 time to fit residues: 9.9306 Evaluate side-chains 42 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0651 time to fit residues: 1.0988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6560 Z= 0.208 Angle : 0.562 5.811 8980 Z= 0.287 Chirality : 0.041 0.119 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.249 17.688 974 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 22.95 % 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: -0.05 (0.28), residues: 940 helix: 1.58 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.25 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.001 0.000 HIS A 695 PHE 0.009 0.001 PHE B 488 TYR 0.005 0.001 TYR B 584 ARG 0.002 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 40 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.714 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1507 time to fit residues: 9.3648 Evaluate side-chains 40 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 30.0000 chunk 66 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 0.0010 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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: 0.4780 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6560 Z= 0.171 Angle : 0.547 5.608 8980 Z= 0.277 Chirality : 0.040 0.109 1094 Planarity : 0.005 0.058 1126 Dihedral : 4.130 17.695 974 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.18 % Allowed : 23.67 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 940 helix: 1.72 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.22 (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 465 TYR 0.004 0.001 TYR B 739 ARG 0.001 0.000 ARG B 705 *********************** 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 42 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.636 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1502 time to fit residues: 9.7956 Evaluate side-chains 41 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4799 moved from start: 0.3145 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= 0.196 Angle : 0.556 5.977 8980 Z= 0.283 Chirality : 0.040 0.115 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.132 17.122 974 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 23.84 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 940 helix: 1.70 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.23 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 732 HIS 0.001 0.000 HIS A 695 PHE 0.008 0.001 PHE A 488 TYR 0.005 0.001 TYR B 584 ARG 0.001 0.000 ARG B 546 ********************** 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 41 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1425 time to fit residues: 9.1193 Evaluate side-chains 41 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.198724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.155688 restraints weight = 7019.638| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.66 r_work: 0.3732 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6560 Z= 0.244 Angle : 0.584 5.624 8980 Z= 0.300 Chirality : 0.041 0.126 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.275 16.446 974 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.18 % Allowed : 23.67 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 940 helix: 1.54 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.24 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 732 HIS 0.001 0.000 HIS A 695 PHE 0.010 0.001 PHE B 488 TYR 0.006 0.001 TYR B 584 ARG 0.002 0.000 ARG B 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1428.33 seconds wall clock time: 28 minutes 15.64 seconds (1695.64 seconds total)