Starting phenix.real_space_refine on Fri Dec 8 02:10:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1y_24812/12_2023/7s1y_24812_updated.pdb" } resolution = 3.6 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= 0.008 sd= 0.074 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 34 5.16 5 Cl 2 4.86 5 C 4338 2.51 5 N 1054 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B TYR 751": "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: 6580 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3263 Classifications: {'peptide': 474} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 457} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3263 Classifications: {'peptide': 474} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 457} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.17, per 1000 atoms: 0.63 Number of scatterers: 6580 At special positions: 0 Unit cell: (107.06, 66.78, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 34 16.00 O 1150 8.00 N 1054 7.00 C 4338 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=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.3 seconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 82U A1303 " pdb=" CB 82U B1303 " Number of C-beta restraints generated: 1648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 68.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.353A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 342 removed outlier: 4.321A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 Processing helix chain 'A' and resid 362 through 398 removed outlier: 3.743A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 424 removed outlier: 4.241A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.962A pdb=" N GLU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 487 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.516A pdb=" N ILE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLY A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 543 removed outlier: 3.672A pdb=" N LEU A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 570 Processing helix chain 'A' and resid 592 through 595 No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 600 through 631 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 652 through 668 Processing helix chain 'A' and resid 672 through 698 Proline residue: A 676 - end of helix removed outlier: 4.476A pdb=" N ASN A 680 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 682 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.924A pdb=" N PHE B 305 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG B 307 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 309 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 4.364A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 360 Processing helix chain 'B' and resid 362 through 398 removed outlier: 3.631A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 removed outlier: 4.173A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 3.890A pdb=" N GLU B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 487 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 503 through 510 removed outlier: 5.848A pdb=" N GLY B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 543 removed outlier: 3.704A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 592 through 595 No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 600 through 631 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 652 through 668 Processing helix chain 'B' and resid 672 through 698 Proline residue: B 676 - end of helix removed outlier: 4.145A pdb=" N ASN B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 682 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 729 Processing helix chain 'B' and resid 732 through 751 445 hydrogen bonds defined for protein. 1275 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: 1.84 Time building geometry restraints manager: 3.34 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: 2040 1.34 - 1.46: 1702 1.46 - 1.58: 2942 1.58 - 1.70: 2 1.70 - 1.81: 50 Bond restraints: 6736 Sorted by residual: bond pdb=" CG PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 1.503 1.346 0.157 3.40e-02 8.65e+02 2.15e+01 bond pdb=" N 82U A1303 " pdb=" CA 82U A1303 " ideal model delta sigma weight residual 1.366 1.442 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" N 82U B1303 " pdb=" CA 82U B1303 " ideal model delta sigma weight residual 1.366 1.439 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CB PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.11e+01 bond pdb=" N PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.51e+00 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 92.75 - 101.04: 14 101.04 - 109.32: 349 109.32 - 117.60: 4500 117.60 - 125.88: 4254 125.88 - 134.16: 105 Bond angle restraints: 9222 Sorted by residual: angle pdb=" CA PRO A 676 " pdb=" N PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 112.00 96.30 15.70 1.40e+00 5.10e-01 1.26e+02 angle pdb=" N PRO A 676 " pdb=" CD PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 103.20 92.75 10.45 1.50e+00 4.44e-01 4.85e+01 angle pdb=" CA PRO A 636 " pdb=" N PRO A 636 " pdb=" CD PRO A 636 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CA PRO A 676 " pdb=" CB PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 104.50 97.20 7.30 1.90e+00 2.77e-01 1.48e+01 angle pdb=" C PRO A 676 " pdb=" CA PRO A 676 " pdb=" CB PRO A 676 " ideal model delta sigma weight residual 110.88 115.84 -4.96 1.41e+00 5.03e-01 1.24e+01 ... (remaining 9217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3427 17.69 - 35.39: 286 35.39 - 53.08: 37 53.08 - 70.77: 5 70.77 - 88.47: 3 Dihedral angle restraints: 3758 sinusoidal: 1134 harmonic: 2624 Sorted by residual: dihedral pdb=" CB CYS B 563 " pdb=" SG CYS B 563 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual 93.00 148.54 -55.54 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA TYR B 711 " pdb=" C TYR B 711 " pdb=" N ASN B 712 " pdb=" CA ASN B 712 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 862 0.053 - 0.106: 214 0.106 - 0.159: 15 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR B 711 " pdb=" N TYR B 711 " pdb=" C TYR B 711 " pdb=" CB TYR B 711 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO A 676 " pdb=" N PRO A 676 " pdb=" C PRO A 676 " pdb=" CB PRO A 676 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1091 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 635 " 0.090 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 636 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 636 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 636 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 675 " 0.084 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO A 676 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 288 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ILE B 288 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B 288 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 289 " -0.010 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.28: 4 2.28 - 3.00: 3876 3.00 - 3.71: 12540 3.71 - 4.43: 17725 4.43 - 5.14: 28771 Nonbonded interactions: 62916 Sorted by model distance: nonbonded pdb=" K K A1301 " pdb=" O5 82U A1303 " model vdw 1.566 2.850 nonbonded pdb=" K K B1301 " pdb=" O5 82U B1303 " model vdw 1.614 2.850 nonbonded pdb=" OG SER A 339 " pdb=" OH TYR A 711 " model vdw 2.133 2.440 nonbonded pdb=" OG SER B 339 " pdb=" OH TYR B 711 " model vdw 2.142 2.440 nonbonded pdb=" OE1 GLU B 485 " pdb=" OG SER B 489 " model vdw 2.313 2.440 ... (remaining 62911 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 group one per residue 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: 1.840 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: 4.100 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.740 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 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 : 0.005 0.166 6736 Z= 0.330 Angle : 0.772 15.702 9222 Z= 0.417 Chirality : 0.044 0.265 1094 Planarity : 0.006 0.131 1158 Dihedral : 12.892 88.467 2098 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.24 % 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: -0.33 (0.28), residues: 944 helix: 0.96 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 287 HIS 0.004 0.001 HIS A 398 PHE 0.025 0.001 PHE A 608 TYR 0.016 0.001 TYR B 739 ARG 0.001 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.862 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1251 time to fit residues: 28.6132 Evaluate side-chains 109 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9008 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6736 Z= 0.195 Angle : 0.622 9.965 9222 Z= 0.317 Chirality : 0.042 0.309 1094 Planarity : 0.005 0.082 1158 Dihedral : 5.895 37.431 1022 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.05 % Favored : 91.74 % Rotamer: Outliers : 2.43 % Allowed : 12.67 % Favored : 84.90 % Cbeta Deviations : 0.24 % 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: -0.30 (0.27), residues: 944 helix: 0.98 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.003 0.001 HIS B 398 PHE 0.025 0.002 PHE B 477 TYR 0.030 0.002 TYR A 739 ARG 0.005 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.881 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1451 time to fit residues: 30.3861 Evaluate side-chains 117 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0706 time to fit residues: 2.3915 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 40.0000 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN B 435 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6736 Z= 0.214 Angle : 0.630 11.033 9222 Z= 0.319 Chirality : 0.042 0.260 1094 Planarity : 0.004 0.070 1158 Dihedral : 5.965 38.982 1022 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 1.04 % Allowed : 18.92 % Favored : 80.03 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.49 (0.27), residues: 944 helix: 0.86 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.70 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 300 HIS 0.002 0.001 HIS B 398 PHE 0.022 0.002 PHE A 285 TYR 0.026 0.002 TYR A 739 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.622 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.1092 time to fit residues: 21.1295 Evaluate side-chains 114 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0642 time to fit residues: 1.3791 ------------------------------------------------------------------------------- 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: 0.7980 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6736 Z= 0.180 Angle : 0.603 10.852 9222 Z= 0.305 Chirality : 0.041 0.240 1094 Planarity : 0.004 0.063 1158 Dihedral : 5.793 37.601 1022 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.94 % Favored : 91.84 % Rotamer: Outliers : 2.43 % Allowed : 20.83 % Favored : 76.74 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.43 (0.27), residues: 944 helix: 0.95 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.79 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 300 HIS 0.002 0.001 HIS B 398 PHE 0.022 0.001 PHE B 285 TYR 0.021 0.001 TYR A 739 ARG 0.003 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.730 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 0.1141 time to fit residues: 22.7236 Evaluate side-chains 116 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0608 time to fit residues: 1.5779 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5564 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6736 Z= 0.208 Angle : 0.617 10.853 9222 Z= 0.313 Chirality : 0.042 0.285 1094 Planarity : 0.004 0.059 1158 Dihedral : 5.877 38.736 1022 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 2.43 % Allowed : 22.92 % Favored : 74.65 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.51 (0.27), residues: 944 helix: 0.88 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.82 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 287 HIS 0.002 0.001 HIS A 398 PHE 0.022 0.001 PHE B 495 TYR 0.019 0.001 TYR B 584 ARG 0.002 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.705 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 126 average time/residue: 0.1160 time to fit residues: 22.4829 Evaluate side-chains 122 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0752 time to fit residues: 1.5948 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 0.3980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6736 Z= 0.239 Angle : 0.657 11.191 9222 Z= 0.333 Chirality : 0.044 0.332 1094 Planarity : 0.004 0.056 1158 Dihedral : 6.109 44.769 1022 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.58 % Favored : 91.21 % Rotamer: Outliers : 1.91 % Allowed : 23.26 % Favored : 74.83 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.61 (0.27), residues: 944 helix: 0.74 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS A 398 PHE 0.018 0.002 PHE B 495 TYR 0.020 0.002 TYR B 584 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.750 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 124 average time/residue: 0.1170 time to fit residues: 22.1619 Evaluate side-chains 114 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0644 time to fit residues: 1.3492 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6736 Z= 0.212 Angle : 0.646 11.106 9222 Z= 0.324 Chirality : 0.044 0.347 1094 Planarity : 0.004 0.054 1158 Dihedral : 5.936 40.270 1022 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.99 % Favored : 92.80 % Rotamer: Outliers : 1.74 % Allowed : 25.17 % Favored : 73.09 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.55 (0.27), residues: 944 helix: 0.85 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.85 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 287 HIS 0.002 0.001 HIS A 398 PHE 0.025 0.001 PHE A 681 TYR 0.016 0.001 TYR A 584 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.725 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 0.1200 time to fit residues: 22.4338 Evaluate side-chains 117 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0677 time to fit residues: 1.6693 ------------------------------------------------------------------------------- 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: 0.0770 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 0.0000 chunk 86 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6736 Z= 0.192 Angle : 0.646 10.570 9222 Z= 0.322 Chirality : 0.043 0.285 1094 Planarity : 0.004 0.053 1158 Dihedral : 5.720 36.942 1022 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 0.87 % Allowed : 26.22 % Favored : 72.92 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.40 (0.27), residues: 944 helix: 0.98 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.82 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 287 HIS 0.001 0.001 HIS A 398 PHE 0.025 0.001 PHE A 681 TYR 0.020 0.001 TYR A 739 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.658 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 120 average time/residue: 0.1247 time to fit residues: 22.6687 Evaluate side-chains 116 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0707 time to fit residues: 1.4466 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6736 Z= 0.242 Angle : 0.684 15.946 9222 Z= 0.339 Chirality : 0.045 0.329 1094 Planarity : 0.004 0.053 1158 Dihedral : 5.955 39.584 1022 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 0.87 % Allowed : 27.78 % Favored : 71.35 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.49 (0.27), residues: 944 helix: 0.88 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.76 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 287 HIS 0.001 0.001 HIS A 398 PHE 0.024 0.002 PHE A 681 TYR 0.018 0.002 TYR A 739 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.1182 time to fit residues: 20.8962 Evaluate side-chains 113 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0637 time to fit residues: 1.1746 ------------------------------------------------------------------------------- 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: 0.0060 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.0870 chunk 74 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6736 Z= 0.216 Angle : 0.698 15.887 9222 Z= 0.340 Chirality : 0.044 0.308 1094 Planarity : 0.004 0.052 1158 Dihedral : 5.839 38.979 1022 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 28.82 % Favored : 71.18 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.49 (0.27), residues: 944 helix: 0.88 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.77 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 287 HIS 0.001 0.001 HIS A 398 PHE 0.027 0.002 PHE A 681 TYR 0.019 0.001 TYR A 739 ARG 0.003 0.000 ARG B 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.690 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1272 time to fit residues: 21.1141 Evaluate side-chains 106 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8900 ------------------------------------------------------------------------------- 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: 0.0970 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 31 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.253701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.223867 restraints weight = 8003.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.228911 restraints weight = 4719.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.232443 restraints weight = 3305.938| |-----------------------------------------------------------------------------| r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6736 Z= 0.211 Angle : 0.676 15.869 9222 Z= 0.333 Chirality : 0.044 0.315 1094 Planarity : 0.004 0.052 1158 Dihedral : 5.831 40.479 1022 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.89 % Favored : 92.90 % Rotamer: Outliers : 0.35 % Allowed : 28.99 % Favored : 70.66 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.45 (0.27), residues: 944 helix: 0.89 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.72 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 287 HIS 0.001 0.000 HIS A 398 PHE 0.028 0.002 PHE A 681 TYR 0.020 0.001 TYR A 739 ARG 0.003 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.30 seconds wall clock time: 27 minutes 15.14 seconds (1635.14 seconds total)