Starting phenix.real_space_refine on Wed Feb 14 01:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgf_31967/02_2024/7vgf_31967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgf_31967/02_2024/7vgf_31967.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/7vgf_31967/02_2024/7vgf_31967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgf_31967/02_2024/7vgf_31967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgf_31967/02_2024/7vgf_31967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgf_31967/02_2024/7vgf_31967_updated.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= -0.001 sd= 0.059 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 P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5284 2.51 5 N 1412 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.59 Number of scatterers: 8280 At special positions: 0 Unit cell: (110.526, 67.938, 133.848, 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) S 20 16.00 P 6 15.00 Mg 2 11.99 O 1556 8.00 N 1412 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 4 sheets defined 65.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 134 through 170 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 186 through 235 removed outlier: 3.883A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 248 through 288 removed outlier: 4.833A pdb=" N LEU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 291 through 338 removed outlier: 4.068A pdb=" N ARG A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 318 " --> pdb=" O TRP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 401 removed outlier: 4.121A pdb=" N ALA A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 450 Proline residue: A 423 - end of helix removed outlier: 5.152A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLN A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 541 through 547 Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.279A pdb=" N GLY A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 611 through 625 Processing helix chain 'A' and resid 641 through 655 Processing helix chain 'A' and resid 667 through 670 No H-bonds generated for 'chain 'A' and resid 667 through 670' Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'B' and resid 134 through 170 Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 186 through 235 removed outlier: 3.882A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 248 through 288 removed outlier: 4.832A pdb=" N LEU B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 291 through 338 removed outlier: 4.069A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 318 " --> pdb=" O TRP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 350 through 401 removed outlier: 4.121A pdb=" N ALA B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 450 Proline residue: B 423 - end of helix removed outlier: 5.152A pdb=" N PHE B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLN B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 541 through 547 Processing helix chain 'B' and resid 562 through 569 removed outlier: 4.280A pdb=" N GLY B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 584 Processing helix chain 'B' and resid 588 through 593 Processing helix chain 'B' and resid 611 through 625 Processing helix chain 'B' and resid 641 through 655 Processing helix chain 'B' and resid 667 through 670 No H-bonds generated for 'chain 'B' and resid 667 through 670' Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing sheet with id= A, first strand: chain 'A' and resid 473 through 475 Processing sheet with id= B, first strand: chain 'A' and resid 683 through 688 removed outlier: 3.557A pdb=" N ALA A 685 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 678 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 687 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 676 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 675 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER A 660 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 503 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 662 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 473 through 475 Processing sheet with id= D, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.557A pdb=" N ALA B 685 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 678 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 687 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 676 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 675 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER B 660 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE B 503 " --> pdb=" O SER B 660 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE B 662 " --> pdb=" O ILE B 503 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2690 1.34 - 1.46: 1056 1.46 - 1.57: 4627 1.57 - 1.69: 8 1.69 - 1.81: 41 Bond restraints: 8422 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.609 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C4 ANP A 901 " pdb=" C5 ANP A 901 " ideal model delta sigma weight residual 1.387 1.471 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.669 1.750 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 8417 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.48: 197 107.48 - 114.63: 5042 114.63 - 121.79: 4608 121.79 - 128.95: 1582 128.95 - 136.11: 33 Bond angle restraints: 11462 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.49 16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" N GLU B 604 " pdb=" CA GLU B 604 " pdb=" C GLU B 604 " ideal model delta sigma weight residual 111.07 106.69 4.38 1.07e+00 8.73e-01 1.68e+01 angle pdb=" N GLU A 604 " pdb=" CA GLU A 604 " pdb=" C GLU A 604 " ideal model delta sigma weight residual 111.07 106.71 4.36 1.07e+00 8.73e-01 1.66e+01 angle pdb=" N VAL A 450 " pdb=" CA VAL A 450 " pdb=" C VAL A 450 " ideal model delta sigma weight residual 112.98 108.30 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" N VAL B 450 " pdb=" CA VAL B 450 " pdb=" C VAL B 450 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 11457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 4665 22.29 - 44.58: 279 44.58 - 66.87: 33 66.87 - 89.16: 12 89.16 - 111.45: 1 Dihedral angle restraints: 4990 sinusoidal: 1836 harmonic: 3154 Sorted by residual: dihedral pdb=" O1A ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PA ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sinusoidal sigma weight residual 83.11 -165.44 -111.45 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA ARG A 520 " pdb=" C ARG A 520 " pdb=" N PHE A 521 " pdb=" CA PHE A 521 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ARG B 520 " pdb=" C ARG B 520 " pdb=" N PHE B 521 " pdb=" CA PHE B 521 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1118 0.050 - 0.100: 225 0.100 - 0.151: 28 0.151 - 0.201: 2 0.201 - 0.251: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" C2' ANP A 901 " pdb=" C1' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" O2' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1371 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 466 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 467 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 466 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 467 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 222 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE B 222 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE B 222 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 223 " -0.009 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 99 2.65 - 3.21: 8167 3.21 - 3.77: 12868 3.77 - 4.34: 16534 4.34 - 4.90: 27091 Nonbonded interactions: 64759 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb="MG MG B 902 " model vdw 2.083 2.170 nonbonded pdb=" OG SER A 512 " pdb="MG MG A 902 " model vdw 2.084 2.170 nonbonded pdb=" O1G ANP B 901 " pdb="MG MG B 902 " model vdw 2.120 2.170 nonbonded pdb=" OG1 THR B 636 " pdb=" O2G ANP B 901 " model vdw 2.210 2.440 nonbonded pdb=" OG SER B 610 " pdb=" OE1 GLU B 613 " model vdw 2.259 2.440 ... (remaining 64754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.310 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.360 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.004 0.144 8422 Z= 0.319 Angle : 0.696 16.463 11462 Z= 0.346 Chirality : 0.040 0.251 1374 Planarity : 0.003 0.043 1456 Dihedral : 14.500 111.448 2970 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % 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: 2.62 (0.26), residues: 1092 helix: 2.84 (0.19), residues: 724 sheet: 1.10 (0.67), residues: 54 loop : -0.91 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 314 HIS 0.002 0.000 HIS A 234 PHE 0.020 0.002 PHE B 214 TYR 0.009 0.001 TYR A 196 ARG 0.003 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8592 (tmmt) cc_final: 0.7919 (ttmm) REVERT: A 559 HIS cc_start: 0.7897 (t-90) cc_final: 0.7455 (t-90) REVERT: B 225 ILE cc_start: 0.8485 (mp) cc_final: 0.8270 (mp) REVERT: B 260 ILE cc_start: 0.7685 (mm) cc_final: 0.7458 (tt) REVERT: B 324 LYS cc_start: 0.8484 (tmmt) cc_final: 0.7915 (ttmt) REVERT: B 327 ASN cc_start: 0.8425 (t0) cc_final: 0.8142 (t0) REVERT: B 392 ILE cc_start: 0.8159 (tp) cc_final: 0.7817 (tt) REVERT: B 559 HIS cc_start: 0.7930 (t-90) cc_final: 0.7507 (t-90) REVERT: B 663 ILE cc_start: 0.7571 (mt) cc_final: 0.7331 (mt) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2078 time to fit residues: 53.3450 Evaluate side-chains 130 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7238 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8422 Z= 0.157 Angle : 0.493 5.026 11462 Z= 0.257 Chirality : 0.038 0.136 1374 Planarity : 0.003 0.031 1456 Dihedral : 7.583 87.985 1250 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.03 % Allowed : 9.07 % Favored : 88.90 % 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: 2.89 (0.26), residues: 1092 helix: 3.08 (0.19), residues: 720 sheet: 1.59 (0.60), residues: 50 loop : -0.91 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 314 HIS 0.003 0.001 HIS A 657 PHE 0.015 0.001 PHE A 240 TYR 0.012 0.001 TYR B 196 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8548 (tmmt) cc_final: 0.7947 (ttmm) REVERT: A 339 ASN cc_start: 0.7998 (m-40) cc_final: 0.7659 (m-40) REVERT: B 260 ILE cc_start: 0.7660 (mm) cc_final: 0.7438 (tt) REVERT: B 324 LYS cc_start: 0.8431 (tmmt) cc_final: 0.7947 (ttmt) REVERT: B 327 ASN cc_start: 0.8421 (t0) cc_final: 0.8130 (t0) REVERT: B 392 ILE cc_start: 0.8168 (tp) cc_final: 0.7847 (tt) REVERT: B 418 PHE cc_start: 0.7029 (t80) cc_final: 0.6829 (t80) outliers start: 17 outliers final: 14 residues processed: 146 average time/residue: 0.1659 time to fit residues: 34.8944 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 83 optimal weight: 0.0010 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8422 Z= 0.184 Angle : 0.476 5.318 11462 Z= 0.252 Chirality : 0.038 0.134 1374 Planarity : 0.003 0.025 1456 Dihedral : 6.755 68.171 1246 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 11.10 % Favored : 86.52 % 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: 2.97 (0.27), residues: 1092 helix: 3.14 (0.19), residues: 720 sheet: 1.87 (0.64), residues: 50 loop : -0.92 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.021 0.002 PHE A 385 TYR 0.011 0.001 TYR B 196 ARG 0.009 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8599 (tmmt) cc_final: 0.8067 (ttmm) REVERT: A 339 ASN cc_start: 0.8250 (m-40) cc_final: 0.8039 (m-40) REVERT: A 409 ASP cc_start: 0.7709 (t0) cc_final: 0.7407 (t0) REVERT: A 493 PHE cc_start: 0.6491 (m-10) cc_final: 0.6262 (m-10) REVERT: A 559 HIS cc_start: 0.7835 (t-90) cc_final: 0.7524 (t-90) REVERT: B 260 ILE cc_start: 0.7736 (mm) cc_final: 0.7510 (tt) REVERT: B 324 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7846 (ttmm) REVERT: B 409 ASP cc_start: 0.7713 (t0) cc_final: 0.7479 (t0) REVERT: B 530 TYR cc_start: 0.6102 (m-80) cc_final: 0.5657 (m-10) REVERT: B 559 HIS cc_start: 0.7965 (t-90) cc_final: 0.7385 (t-90) REVERT: B 571 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 633 ASP cc_start: 0.7373 (t0) cc_final: 0.7073 (m-30) outliers start: 20 outliers final: 18 residues processed: 142 average time/residue: 0.1819 time to fit residues: 36.6161 Evaluate side-chains 138 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8422 Z= 0.177 Angle : 0.482 8.679 11462 Z= 0.253 Chirality : 0.038 0.131 1374 Planarity : 0.003 0.023 1456 Dihedral : 6.521 61.183 1246 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.51 % Allowed : 13.25 % Favored : 84.25 % 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: 3.00 (0.27), residues: 1092 helix: 3.15 (0.19), residues: 720 sheet: 1.99 (0.64), residues: 50 loop : -0.89 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.018 0.001 PHE B 418 TYR 0.012 0.001 TYR B 196 ARG 0.008 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.934 Fit side-chains REVERT: A 324 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8099 (ttmm) REVERT: A 339 ASN cc_start: 0.8325 (m-40) cc_final: 0.7962 (m110) REVERT: A 409 ASP cc_start: 0.7700 (t0) cc_final: 0.7405 (t0) REVERT: A 493 PHE cc_start: 0.6617 (m-10) cc_final: 0.6202 (m-10) REVERT: A 559 HIS cc_start: 0.7896 (t-90) cc_final: 0.7572 (t-90) REVERT: B 224 ARG cc_start: 0.7720 (ttm110) cc_final: 0.6920 (mtm-85) REVERT: B 324 LYS cc_start: 0.8463 (tmmt) cc_final: 0.8056 (ttmt) REVERT: B 409 ASP cc_start: 0.7780 (t0) cc_final: 0.7557 (t0) REVERT: B 530 TYR cc_start: 0.6093 (m-80) cc_final: 0.5656 (m-10) REVERT: B 559 HIS cc_start: 0.7945 (t-90) cc_final: 0.7379 (t-90) outliers start: 21 outliers final: 18 residues processed: 134 average time/residue: 0.1821 time to fit residues: 35.4090 Evaluate side-chains 137 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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: 0.7333 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8422 Z= 0.173 Angle : 0.480 8.080 11462 Z= 0.252 Chirality : 0.038 0.179 1374 Planarity : 0.003 0.029 1456 Dihedral : 6.242 56.197 1246 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.10 % Allowed : 14.08 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.27), residues: 1092 helix: 2.96 (0.19), residues: 734 sheet: 1.93 (0.65), residues: 50 loop : -1.17 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.012 0.001 PHE A 385 TYR 0.011 0.001 TYR B 196 ARG 0.008 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.094 Fit side-chains REVERT: A 324 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8066 (ttmm) REVERT: A 339 ASN cc_start: 0.8428 (m-40) cc_final: 0.8090 (m110) REVERT: A 409 ASP cc_start: 0.7697 (t0) cc_final: 0.7376 (t0) REVERT: A 559 HIS cc_start: 0.7905 (t-90) cc_final: 0.7554 (t-90) REVERT: B 324 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8063 (ttmt) REVERT: B 530 TYR cc_start: 0.6107 (m-80) cc_final: 0.5683 (m-10) REVERT: B 559 HIS cc_start: 0.7924 (t-90) cc_final: 0.7344 (t-90) outliers start: 26 outliers final: 22 residues processed: 135 average time/residue: 0.1836 time to fit residues: 36.0385 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7387 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8422 Z= 0.225 Angle : 0.524 7.802 11462 Z= 0.281 Chirality : 0.040 0.191 1374 Planarity : 0.003 0.027 1456 Dihedral : 6.225 58.960 1246 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.22 % Allowed : 14.20 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.27), residues: 1092 helix: 2.80 (0.19), residues: 734 sheet: 1.94 (0.70), residues: 50 loop : -1.24 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.005 0.001 HIS B 588 PHE 0.017 0.002 PHE B 418 TYR 0.010 0.001 TYR B 196 ARG 0.009 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.935 Fit side-chains REVERT: A 324 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8099 (ttmm) REVERT: A 339 ASN cc_start: 0.8564 (m-40) cc_final: 0.8262 (m110) REVERT: A 409 ASP cc_start: 0.7785 (t0) cc_final: 0.7577 (t0) REVERT: A 559 HIS cc_start: 0.7900 (t-90) cc_final: 0.7547 (t-90) REVERT: B 324 LYS cc_start: 0.8437 (tmmt) cc_final: 0.8065 (ttmt) REVERT: B 530 TYR cc_start: 0.6238 (m-80) cc_final: 0.5815 (m-10) REVERT: B 559 HIS cc_start: 0.7950 (t-90) cc_final: 0.7362 (t-90) outliers start: 27 outliers final: 24 residues processed: 138 average time/residue: 0.1632 time to fit residues: 33.4804 Evaluate side-chains 150 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8422 Z= 0.155 Angle : 0.477 7.212 11462 Z= 0.255 Chirality : 0.039 0.208 1374 Planarity : 0.003 0.026 1456 Dihedral : 5.925 55.196 1246 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.22 % Allowed : 15.39 % Favored : 81.38 % 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: 2.68 (0.27), residues: 1092 helix: 2.88 (0.19), residues: 734 sheet: 1.83 (0.68), residues: 50 loop : -1.14 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.002 0.001 HIS B 588 PHE 0.013 0.001 PHE B 418 TYR 0.011 0.001 TYR A 196 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.874 Fit side-chains REVERT: A 324 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8064 (ttmm) REVERT: A 339 ASN cc_start: 0.8454 (m-40) cc_final: 0.8212 (m110) REVERT: A 409 ASP cc_start: 0.7762 (t0) cc_final: 0.7452 (t0) REVERT: A 427 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6430 (tp) REVERT: A 493 PHE cc_start: 0.6737 (m-10) cc_final: 0.6167 (m-10) REVERT: A 559 HIS cc_start: 0.7875 (t-90) cc_final: 0.7532 (t-90) REVERT: B 324 LYS cc_start: 0.8406 (tmmt) cc_final: 0.8057 (ttmt) REVERT: B 339 ASN cc_start: 0.8497 (m-40) cc_final: 0.8019 (m110) REVERT: B 530 TYR cc_start: 0.6123 (m-80) cc_final: 0.5720 (m-10) REVERT: B 559 HIS cc_start: 0.7903 (t-90) cc_final: 0.7334 (t-90) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.1573 time to fit residues: 32.5281 Evaluate side-chains 143 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.0270 chunk 67 optimal weight: 0.0270 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.0010 chunk 92 optimal weight: 1.9990 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8422 Z= 0.145 Angle : 0.496 6.863 11462 Z= 0.263 Chirality : 0.038 0.217 1374 Planarity : 0.003 0.024 1456 Dihedral : 5.709 53.859 1246 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 16.11 % Favored : 81.26 % 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: 2.77 (0.27), residues: 1092 helix: 2.94 (0.19), residues: 734 sheet: 1.88 (0.67), residues: 50 loop : -1.08 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.001 0.000 HIS A 588 PHE 0.013 0.001 PHE B 214 TYR 0.013 0.001 TYR A 196 ARG 0.006 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.900 Fit side-chains REVERT: A 324 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8060 (ttmm) REVERT: A 339 ASN cc_start: 0.8388 (m-40) cc_final: 0.8118 (m110) REVERT: A 409 ASP cc_start: 0.7741 (t0) cc_final: 0.7418 (t0) REVERT: A 493 PHE cc_start: 0.6743 (m-10) cc_final: 0.6296 (m-10) REVERT: A 559 HIS cc_start: 0.7895 (t-90) cc_final: 0.7569 (t-90) REVERT: B 324 LYS cc_start: 0.8358 (tmmt) cc_final: 0.7855 (ttmm) REVERT: B 418 PHE cc_start: 0.7223 (t80) cc_final: 0.7003 (t80) REVERT: B 530 TYR cc_start: 0.6062 (m-80) cc_final: 0.5671 (m-10) REVERT: B 559 HIS cc_start: 0.7895 (t-90) cc_final: 0.7581 (t-90) outliers start: 22 outliers final: 18 residues processed: 136 average time/residue: 0.1576 time to fit residues: 31.5606 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.1980 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7303 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8422 Z= 0.151 Angle : 0.487 6.930 11462 Z= 0.258 Chirality : 0.039 0.206 1374 Planarity : 0.003 0.024 1456 Dihedral : 5.637 53.753 1246 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.27 % Allowed : 16.83 % Favored : 80.91 % 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: 2.81 (0.27), residues: 1092 helix: 2.97 (0.19), residues: 734 sheet: 1.94 (0.66), residues: 50 loop : -1.07 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 314 HIS 0.002 0.001 HIS B 588 PHE 0.012 0.001 PHE B 214 TYR 0.013 0.001 TYR A 196 ARG 0.006 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.831 Fit side-chains REVERT: A 324 LYS cc_start: 0.8490 (tmmt) cc_final: 0.8057 (ttmm) REVERT: A 339 ASN cc_start: 0.8366 (m-40) cc_final: 0.8089 (m110) REVERT: A 493 PHE cc_start: 0.6795 (m-10) cc_final: 0.6315 (m-10) REVERT: A 559 HIS cc_start: 0.7901 (t-90) cc_final: 0.7580 (t-90) REVERT: B 324 LYS cc_start: 0.8340 (tmmt) cc_final: 0.7843 (ttmm) REVERT: B 530 TYR cc_start: 0.6047 (m-80) cc_final: 0.5660 (m-10) REVERT: B 559 HIS cc_start: 0.7900 (t-90) cc_final: 0.7590 (t-90) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.1550 time to fit residues: 29.7381 Evaluate side-chains 136 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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: 0.7291 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8422 Z= 0.149 Angle : 0.489 6.809 11462 Z= 0.258 Chirality : 0.039 0.205 1374 Planarity : 0.003 0.024 1456 Dihedral : 5.554 52.614 1246 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 17.18 % Favored : 80.55 % 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: 2.83 (0.27), residues: 1092 helix: 2.97 (0.19), residues: 734 sheet: 2.10 (0.66), residues: 50 loop : -1.05 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.002 0.000 HIS B 588 PHE 0.012 0.001 PHE B 418 TYR 0.013 0.001 TYR A 196 ARG 0.006 0.000 ARG B 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.934 Fit side-chains REVERT: A 324 LYS cc_start: 0.8485 (tmmt) cc_final: 0.8055 (ttmm) REVERT: A 339 ASN cc_start: 0.8362 (m-40) cc_final: 0.8057 (m110) REVERT: A 493 PHE cc_start: 0.6812 (m-10) cc_final: 0.6326 (m-10) REVERT: A 559 HIS cc_start: 0.7908 (t-90) cc_final: 0.7601 (t-90) REVERT: B 260 ILE cc_start: 0.7724 (mm) cc_final: 0.7468 (tt) REVERT: B 324 LYS cc_start: 0.8304 (tmmt) cc_final: 0.7806 (ttmm) REVERT: B 392 ILE cc_start: 0.8103 (tp) cc_final: 0.7808 (tt) REVERT: B 559 HIS cc_start: 0.7903 (t-90) cc_final: 0.7559 (t-90) REVERT: B 560 ASN cc_start: 0.7997 (m110) cc_final: 0.7617 (m-40) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.1618 time to fit residues: 31.2843 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.166216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141654 restraints weight = 11606.311| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.04 r_work: 0.3656 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8422 Z= 0.169 Angle : 0.497 6.882 11462 Z= 0.263 Chirality : 0.039 0.214 1374 Planarity : 0.003 0.025 1456 Dihedral : 5.605 52.776 1246 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.03 % Allowed : 17.54 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.26), residues: 1092 helix: 2.96 (0.19), residues: 734 sheet: 2.14 (0.66), residues: 50 loop : -1.02 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.026 0.001 PHE A 262 TYR 0.012 0.001 TYR A 196 ARG 0.006 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.41 seconds wall clock time: 35 minutes 47.35 seconds (2147.35 seconds total)