Starting phenix.real_space_refine on Wed Jan 17 23:17:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwt_35779/01_2024/8iwt_35779_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4345 2.51 5 N 1137 2.21 5 O 1281 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6820 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6815 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 855} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.01, per 1000 atoms: 0.59 Number of scatterers: 6820 At special positions: 0 Unit cell: (91.56, 94.08, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Mg 1 11.99 F 3 9.00 O 1281 8.00 N 1137 7.00 C 4345 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 9 sheets defined 50.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.824A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 100 through 131 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.891A pdb=" N VAL A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 304 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.311A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.690A pdb=" N LYS A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 646 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 722 Processing helix chain 'A' and resid 731 through 741 Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 773 through 800 Processing helix chain 'A' and resid 806 through 827 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 904 removed outlier: 4.016A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 143 removed outlier: 3.863A pdb=" N CYS A 141 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 removed outlier: 4.620A pdb=" N ILE A 657 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET A 641 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 659 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 643 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 661 " --> pdb=" O GLY A 643 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A 565 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER A 349 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 567 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.694A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 476 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 415 through 417 Processing sheet with id= F, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.628A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 593 through 595 removed outlier: 6.625A pdb=" N VAL A 616 " --> pdb=" O VAL A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.734A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.303A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1062 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: 2.23 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1152 1.32 - 1.44: 1618 1.44 - 1.56: 4070 1.56 - 1.69: 3 1.69 - 1.81: 84 Bond restraints: 6927 Sorted by residual: bond pdb=" CA LYS A 351 " pdb=" C LYS A 351 " ideal model delta sigma weight residual 1.525 1.467 0.059 1.02e-02 9.61e+03 3.30e+01 bond pdb=" BE BEF A1001 " pdb=" F2 BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.24e-02 6.50e+03 1.71e+01 bond pdb=" BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CA THR A 352 " pdb=" C THR A 352 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 ... (remaining 6922 not shown) Histogram of bond angle deviations from ideal: 97.72 - 104.97: 131 104.97 - 112.22: 3628 112.22 - 119.48: 2273 119.48 - 126.73: 3283 126.73 - 133.98: 65 Bond angle restraints: 9380 Sorted by residual: angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 110.53 97.72 12.81 1.29e+00 6.01e-01 9.86e+01 angle pdb=" N SER A 901 " pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 110.97 104.48 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" F2 BEF A1001 " pdb=" BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.21 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N PRO A 805 " pdb=" CA PRO A 805 " pdb=" C PRO A 805 " ideal model delta sigma weight residual 112.47 120.59 -8.12 2.06e+00 2.36e-01 1.55e+01 ... (remaining 9375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3622 16.92 - 33.84: 450 33.84 - 50.76: 130 50.76 - 67.68: 21 67.68 - 84.60: 9 Dihedral angle restraints: 4232 sinusoidal: 1666 harmonic: 2566 Sorted by residual: dihedral pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " pdb=" CG ASP A 757 " pdb=" OD1 ASP A 757 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 403 " pdb=" CD ARG A 403 " pdb=" NE ARG A 403 " pdb=" CZ ARG A 403 " ideal model delta sinusoidal sigma weight residual -180.00 -137.43 -42.57 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" CA LYS A 327 " pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " pdb=" CD LYS A 327 " ideal model delta sinusoidal sigma weight residual 180.00 120.42 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 945 0.054 - 0.108: 165 0.108 - 0.162: 14 0.162 - 0.217: 3 0.217 - 0.271: 2 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CA PRO A 805 " pdb=" N PRO A 805 " pdb=" C PRO A 805 " pdb=" CB PRO A 805 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 18 " pdb=" CA ILE A 18 " pdb=" CG1 ILE A 18 " pdb=" CG2 ILE A 18 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1126 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 804 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 805 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 253 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 254 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.039 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO A 453 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.032 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 14 2.33 - 2.97: 3265 2.97 - 3.61: 10282 3.61 - 4.26: 14916 4.26 - 4.90: 25521 Nonbonded interactions: 53998 Sorted by model distance: nonbonded pdb=" OD2 ASP A 350 " pdb=" F1 BEF A1001 " model vdw 1.687 2.390 nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.757 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb=" BE BEF A1001 " model vdw 1.815 1.936 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.071 2.170 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 2.104 2.170 ... (remaining 53993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.550 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: 9.780 Check model and map are aligned: 0.140 Set scattering table: 0.060 Process input model: 22.350 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 0.103 6927 Z= 0.284 Angle : 0.633 13.749 9380 Z= 0.371 Chirality : 0.041 0.271 1129 Planarity : 0.006 0.119 1185 Dihedral : 16.196 84.605 2572 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.70 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 23.27 % Favored : 76.21 % 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: 2.49 (0.30), residues: 889 helix: 2.56 (0.23), residues: 510 sheet: 0.43 (0.53), residues: 101 loop : 0.46 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 460 HIS 0.002 0.000 HIS A 149 PHE 0.019 0.001 PHE A 57 TYR 0.007 0.001 TYR A 510 ARG 0.007 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.788 Fit side-chains REVERT: A 57 PHE cc_start: 0.7653 (t80) cc_final: 0.7334 (t80) outliers start: 4 outliers final: 1 residues processed: 110 average time/residue: 0.1939 time to fit residues: 28.3226 Evaluate side-chains 102 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 0.0040 chunk 45 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 6927 Z= 0.171 Angle : 0.462 8.055 9380 Z= 0.244 Chirality : 0.040 0.271 1129 Planarity : 0.006 0.119 1185 Dihedral : 3.410 24.242 940 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.41 % Rotamer: Outliers : 1.57 % Allowed : 23.14 % Favored : 75.29 % 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: 2.46 (0.30), residues: 889 helix: 2.65 (0.23), residues: 502 sheet: 0.32 (0.51), residues: 108 loop : 0.33 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 60 HIS 0.002 0.000 HIS A 53 PHE 0.008 0.001 PHE A 538 TYR 0.006 0.001 TYR A 272 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.765 Fit side-chains REVERT: A 146 LYS cc_start: 0.8175 (pptt) cc_final: 0.7933 (pptt) REVERT: A 281 MET cc_start: 0.6971 (mmt) cc_final: 0.6058 (mmt) REVERT: A 686 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5680 (mtm) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 0.2095 time to fit residues: 30.5511 Evaluate side-chains 102 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 GLN A 829 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 6927 Z= 0.380 Angle : 0.656 9.213 9380 Z= 0.349 Chirality : 0.045 0.261 1129 Planarity : 0.006 0.119 1185 Dihedral : 4.526 21.378 939 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 4.58 % Allowed : 20.52 % Favored : 74.90 % 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: 1.39 (0.29), residues: 889 helix: 1.74 (0.23), residues: 498 sheet: -0.26 (0.44), residues: 124 loop : 0.10 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 285 HIS 0.006 0.002 HIS A 394 PHE 0.023 0.002 PHE A 63 TYR 0.015 0.002 TYR A 272 ARG 0.025 0.001 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 0.771 Fit side-chains REVERT: A 229 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: A 402 SER cc_start: 0.8803 (m) cc_final: 0.8592 (p) REVERT: A 641 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7393 (ttt) outliers start: 35 outliers final: 15 residues processed: 136 average time/residue: 0.2128 time to fit residues: 37.7759 Evaluate side-chains 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 841 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6927 Z= 0.238 Angle : 0.535 8.454 9380 Z= 0.281 Chirality : 0.041 0.262 1129 Planarity : 0.006 0.120 1185 Dihedral : 4.111 19.014 939 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.25 % Favored : 97.41 % Rotamer: Outliers : 3.92 % Allowed : 21.31 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 889 helix: 1.88 (0.23), residues: 499 sheet: -0.35 (0.44), residues: 119 loop : 0.13 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.004 0.001 HIS A 149 PHE 0.016 0.002 PHE A 57 TYR 0.012 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.674 Fit side-chains REVERT: A 79 PHE cc_start: 0.7758 (t80) cc_final: 0.7511 (t80) REVERT: A 93 ILE cc_start: 0.8408 (pt) cc_final: 0.8037 (mt) REVERT: A 249 GLN cc_start: 0.7195 (pt0) cc_final: 0.6876 (pt0) REVERT: A 281 MET cc_start: 0.7146 (mmt) cc_final: 0.6556 (mmt) REVERT: A 402 SER cc_start: 0.8801 (m) cc_final: 0.8601 (p) outliers start: 30 outliers final: 21 residues processed: 134 average time/residue: 0.1965 time to fit residues: 34.7994 Evaluate side-chains 125 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 6927 Z= 0.248 Angle : 0.543 10.609 9380 Z= 0.284 Chirality : 0.041 0.268 1129 Planarity : 0.006 0.120 1185 Dihedral : 4.044 19.357 939 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 3.53 % Allowed : 22.09 % Favored : 74.38 % 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: 1.46 (0.29), residues: 889 helix: 1.85 (0.23), residues: 499 sheet: -0.37 (0.44), residues: 119 loop : 0.06 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.003 0.001 HIS A 149 PHE 0.015 0.002 PHE A 57 TYR 0.011 0.001 TYR A 272 ARG 0.006 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.822 Fit side-chains REVERT: A 79 PHE cc_start: 0.7755 (t80) cc_final: 0.7485 (t80) REVERT: A 93 ILE cc_start: 0.8392 (pt) cc_final: 0.8168 (mt) REVERT: A 281 MET cc_start: 0.7419 (mmt) cc_final: 0.6922 (mmt) REVERT: A 861 PHE cc_start: 0.6600 (m-80) cc_final: 0.6393 (m-80) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.1878 time to fit residues: 32.2922 Evaluate side-chains 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 6927 Z= 0.264 Angle : 0.545 8.952 9380 Z= 0.286 Chirality : 0.042 0.261 1129 Planarity : 0.006 0.120 1185 Dihedral : 4.079 19.969 939 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.81 % Favored : 96.85 % Rotamer: Outliers : 3.92 % Allowed : 22.61 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 889 helix: 1.79 (0.23), residues: 498 sheet: -0.47 (0.44), residues: 119 loop : -0.04 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 PHE 0.015 0.002 PHE A 57 TYR 0.011 0.001 TYR A 272 ARG 0.006 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.809 Fit side-chains REVERT: A 79 PHE cc_start: 0.7722 (t80) cc_final: 0.7503 (t80) REVERT: A 281 MET cc_start: 0.7505 (mmt) cc_final: 0.7150 (mmt) REVERT: A 671 GLU cc_start: 0.8256 (tp30) cc_final: 0.7961 (tp30) REVERT: A 861 PHE cc_start: 0.6664 (m-80) cc_final: 0.6296 (m-80) outliers start: 30 outliers final: 25 residues processed: 126 average time/residue: 0.2049 time to fit residues: 34.2191 Evaluate side-chains 124 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6927 Z= 0.219 Angle : 0.516 7.901 9380 Z= 0.270 Chirality : 0.041 0.265 1129 Planarity : 0.005 0.120 1185 Dihedral : 3.917 18.611 939 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.08 % Rotamer: Outliers : 3.40 % Allowed : 23.66 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 889 helix: 1.93 (0.23), residues: 498 sheet: -0.43 (0.45), residues: 119 loop : 0.02 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 PHE 0.018 0.001 PHE A 57 TYR 0.010 0.001 TYR A 272 ARG 0.005 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.753 Fit side-chains REVERT: A 53 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5430 (t-90) REVERT: A 79 PHE cc_start: 0.7706 (t80) cc_final: 0.7483 (t80) REVERT: A 281 MET cc_start: 0.7357 (mmt) cc_final: 0.7030 (mmt) REVERT: A 806 ARG cc_start: 0.5914 (ttt180) cc_final: 0.5383 (ptm160) REVERT: A 860 TYR cc_start: 0.7008 (m-10) cc_final: 0.6632 (m-10) REVERT: A 861 PHE cc_start: 0.6643 (m-80) cc_final: 0.6267 (m-80) outliers start: 26 outliers final: 23 residues processed: 125 average time/residue: 0.1885 time to fit residues: 31.5693 Evaluate side-chains 123 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6927 Z= 0.214 Angle : 0.520 7.708 9380 Z= 0.272 Chirality : 0.041 0.265 1129 Planarity : 0.005 0.120 1185 Dihedral : 3.895 18.584 939 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.70 % Favored : 96.96 % Rotamer: Outliers : 4.18 % Allowed : 22.88 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 889 helix: 1.95 (0.23), residues: 500 sheet: -0.24 (0.47), residues: 110 loop : -0.03 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 285 HIS 0.006 0.001 HIS A 53 PHE 0.014 0.001 PHE A 57 TYR 0.009 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.904 Fit side-chains REVERT: A 79 PHE cc_start: 0.7690 (t80) cc_final: 0.7467 (t80) REVERT: A 443 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: A 806 ARG cc_start: 0.5916 (ttt180) cc_final: 0.5415 (ptm160) REVERT: A 860 TYR cc_start: 0.7001 (m-10) cc_final: 0.6694 (m-10) REVERT: A 861 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6263 (m-80) outliers start: 32 outliers final: 26 residues processed: 127 average time/residue: 0.2154 time to fit residues: 36.7450 Evaluate side-chains 127 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 861 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.0370 chunk 58 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6927 Z= 0.217 Angle : 0.526 9.784 9380 Z= 0.274 Chirality : 0.041 0.265 1129 Planarity : 0.005 0.119 1185 Dihedral : 3.876 18.337 939 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 4.18 % Allowed : 23.01 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.29), residues: 889 helix: 1.98 (0.23), residues: 500 sheet: -0.28 (0.47), residues: 110 loop : -0.03 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 285 HIS 0.003 0.001 HIS A 53 PHE 0.020 0.001 PHE A 57 TYR 0.009 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.774 Fit side-chains REVERT: A 53 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.4720 (t-90) REVERT: A 427 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 535 GLN cc_start: 0.8224 (mp10) cc_final: 0.7859 (mp10) REVERT: A 806 ARG cc_start: 0.5932 (ttt180) cc_final: 0.5424 (ptm160) REVERT: A 860 TYR cc_start: 0.6991 (m-10) cc_final: 0.6707 (m-10) REVERT: A 861 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6237 (m-80) outliers start: 32 outliers final: 27 residues processed: 126 average time/residue: 0.1912 time to fit residues: 32.5365 Evaluate side-chains 130 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 861 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6927 Z= 0.223 Angle : 0.531 9.242 9380 Z= 0.277 Chirality : 0.041 0.265 1129 Planarity : 0.005 0.119 1185 Dihedral : 3.881 18.340 939 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 4.05 % Allowed : 23.14 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 889 helix: 1.97 (0.23), residues: 500 sheet: -0.25 (0.47), residues: 110 loop : -0.03 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.008 0.001 HIS A 53 PHE 0.018 0.001 PHE A 57 TYR 0.009 0.001 TYR A 272 ARG 0.004 0.000 ARG A 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.823 Fit side-chains REVERT: A 427 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 535 GLN cc_start: 0.8209 (mp10) cc_final: 0.7814 (mp10) REVERT: A 806 ARG cc_start: 0.5935 (ttt180) cc_final: 0.5423 (ptm160) REVERT: A 860 TYR cc_start: 0.7006 (m-10) cc_final: 0.6655 (m-80) REVERT: A 861 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6230 (m-80) outliers start: 31 outliers final: 28 residues processed: 122 average time/residue: 0.2946 time to fit residues: 49.6227 Evaluate side-chains 130 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 861 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0050 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 149 HIS A 633 GLN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127604 restraints weight = 8207.697| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.81 r_work: 0.3471 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6927 Z= 0.192 Angle : 0.513 8.580 9380 Z= 0.267 Chirality : 0.041 0.266 1129 Planarity : 0.005 0.119 1185 Dihedral : 3.773 17.118 939 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.08 % Rotamer: Outliers : 3.40 % Allowed : 23.66 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 889 helix: 2.25 (0.24), residues: 488 sheet: -0.22 (0.47), residues: 111 loop : 0.02 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 766 HIS 0.009 0.001 HIS A 53 PHE 0.019 0.001 PHE A 57 TYR 0.008 0.001 TYR A 510 ARG 0.004 0.000 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.90 seconds wall clock time: 37 minutes 34.84 seconds (2254.84 seconds total)