Starting phenix.real_space_refine on Thu Mar 14 08:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjz_21221/03_2024/6vjz_21221.pdb" } resolution = 4.3 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5875 2.51 5 N 1477 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 124": "OE1" <-> "OE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8996 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1355 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 20, 'TRANS': 582} Chain breaks: 4 Chain: "D" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 375 Classifications: {'peptide': 45} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 40} Time building chain proxies: 5.14, per 1000 atoms: 0.57 Number of scatterers: 8996 At special positions: 0 Unit cell: (103.95, 101.25, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1601 8.00 N 1477 7.00 C 5875 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: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.969A pdb=" N VAL C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 41' Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.752A pdb=" N LEU C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 86 Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 117 through 134 removed outlier: 3.692A pdb=" N LEU C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 166 removed outlier: 4.099A pdb=" N ILE C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 Proline residue: C 178 - end of helix Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 75 through 98 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 99 through 100 No H-bonds generated for 'chain 'B' and resid 99 through 100' Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 135 Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.888A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 3.652A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 297 through 324 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.643A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.610A pdb=" N PHE A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.655A pdb=" N ALA A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.720A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 206 through 223 removed outlier: 3.902A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 315 through 331 removed outlier: 4.230A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 4.025A pdb=" N ALA A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.842A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 4.088A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.907A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.693A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.866A pdb=" N ILE A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.687A pdb=" N THR A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 removed outlier: 4.074A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.937A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.661A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.506A pdb=" N VAL A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.608A pdb=" N HIS A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 665 through 686 removed outlier: 3.779A pdb=" N THR A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 753 Processing helix chain 'D' and resid 763 through 777 removed outlier: 3.579A pdb=" N VAL D 777 " --> pdb=" O VAL D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 789 removed outlier: 4.274A pdb=" N ASP D 788 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1890 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: 2.60 Time building geometry restraints manager: 4.03 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: 2775 1.34 - 1.46: 2192 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 9221 Sorted by residual: bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.14e-02 7.69e+03 7.54e+00 bond pdb=" C ALA A 521 " pdb=" N PRO A 522 " ideal model delta sigma weight residual 1.337 1.305 0.033 1.24e-02 6.50e+03 6.88e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.339 -0.018 1.00e-02 1.00e+04 3.14e+00 bond pdb=" C HIS B 101 " pdb=" O HIS B 101 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.07e-02 8.73e+03 2.29e+00 bond pdb=" CB VAL A 658 " pdb=" CG1 VAL A 658 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 ... (remaining 9216 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.33: 147 105.33 - 112.54: 4798 112.54 - 119.75: 3100 119.75 - 126.95: 4340 126.95 - 134.16: 106 Bond angle restraints: 12491 Sorted by residual: angle pdb=" N GLY C 64 " pdb=" CA GLY C 64 " pdb=" C GLY C 64 " ideal model delta sigma weight residual 114.16 104.82 9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C PRO D 757 " pdb=" N ASP D 758 " pdb=" CA ASP D 758 " ideal model delta sigma weight residual 121.70 129.64 -7.94 1.80e+00 3.09e-01 1.95e+01 angle pdb=" CA TYR B 104 " pdb=" C TYR B 104 " pdb=" N PHE B 105 " ideal model delta sigma weight residual 114.59 120.13 -5.54 1.48e+00 4.57e-01 1.40e+01 angle pdb=" C TYR B 104 " pdb=" N PHE B 105 " pdb=" CA PHE B 105 " ideal model delta sigma weight residual 122.42 116.63 5.79 1.55e+00 4.16e-01 1.40e+01 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 112.48 116.81 -4.33 1.21e+00 6.83e-01 1.28e+01 ... (remaining 12486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4806 16.75 - 33.51: 518 33.51 - 50.26: 93 50.26 - 67.02: 18 67.02 - 83.77: 12 Dihedral angle restraints: 5447 sinusoidal: 2189 harmonic: 3258 Sorted by residual: dihedral pdb=" CA TYR C 63 " pdb=" C TYR C 63 " pdb=" N GLY C 64 " pdb=" CA GLY C 64 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER A 245 " pdb=" C SER A 245 " pdb=" N ASP A 246 " pdb=" CA ASP A 246 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1199 0.065 - 0.131: 179 0.131 - 0.196: 9 0.196 - 0.262: 0 0.262 - 0.327: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA LEU A 252 " pdb=" N LEU A 252 " pdb=" C LEU A 252 " pdb=" CB LEU A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL D 777 " pdb=" CA VAL D 777 " pdb=" CG1 VAL D 777 " pdb=" CG2 VAL D 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA THR D 778 " pdb=" N THR D 778 " pdb=" C THR D 778 " pdb=" CB THR D 778 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1385 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 100 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C PHE B 100 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE B 100 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS B 101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 758 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 759 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 759 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 759 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 305 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C TRP B 305 " 0.029 2.00e-02 2.50e+03 pdb=" O TRP B 305 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 306 " -0.010 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1090 2.74 - 3.28: 10487 3.28 - 3.82: 14944 3.82 - 4.36: 17123 4.36 - 4.90: 26922 Nonbonded interactions: 70566 Sorted by model distance: nonbonded pdb=" O TYR A 107 " pdb=" OG SER A 110 " model vdw 2.195 2.440 nonbonded pdb=" O GLU A 463 " pdb=" NZ LYS A 465 " model vdw 2.204 2.520 nonbonded pdb=" O PHE B 95 " pdb=" OG SER B 98 " model vdw 2.214 2.440 nonbonded pdb=" O GLN B 312 " pdb=" OG1 THR B 315 " model vdw 2.222 2.440 nonbonded pdb=" O LEU B 118 " pdb=" ND1 HIS B 122 " model vdw 2.223 2.520 ... (remaining 70561 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 1.380 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.480 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.006 0.058 9221 Z= 0.409 Angle : 0.832 9.345 12491 Z= 0.485 Chirality : 0.046 0.327 1388 Planarity : 0.005 0.059 1546 Dihedral : 14.502 83.769 3343 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 0.10 % Allowed : 9.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -3.21 (0.21), residues: 1073 helix: -1.58 (0.15), residues: 826 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 541 HIS 0.005 0.002 HIS B 122 PHE 0.019 0.002 PHE A 59 TYR 0.028 0.002 TYR B 18 ARG 0.004 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8540 (t60) cc_final: 0.7984 (t60) REVERT: C 80 HIS cc_start: 0.8596 (m90) cc_final: 0.7780 (m90) REVERT: C 108 MET cc_start: 0.8411 (mmp) cc_final: 0.8193 (mmm) REVERT: C 171 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7750 (mm-30) REVERT: C 176 PHE cc_start: 0.8060 (p90) cc_final: 0.7729 (p90) REVERT: C 177 MET cc_start: 0.8564 (tmm) cc_final: 0.8223 (tmm) REVERT: C 184 TYR cc_start: 0.8408 (t80) cc_final: 0.8118 (t80) REVERT: B 5 ASN cc_start: 0.7504 (p0) cc_final: 0.6466 (t0) REVERT: B 9 GLN cc_start: 0.8546 (mt0) cc_final: 0.8254 (mt0) REVERT: B 61 LEU cc_start: 0.9519 (mt) cc_final: 0.9126 (tt) REVERT: B 88 PHE cc_start: 0.8664 (m-80) cc_final: 0.8404 (m-80) REVERT: B 92 ASN cc_start: 0.8623 (m-40) cc_final: 0.7918 (m-40) REVERT: B 95 PHE cc_start: 0.8335 (t80) cc_final: 0.7989 (t80) REVERT: B 106 PHE cc_start: 0.8303 (m-80) cc_final: 0.7603 (p90) REVERT: B 114 LEU cc_start: 0.9257 (tp) cc_final: 0.8857 (tp) REVERT: B 119 LYS cc_start: 0.9493 (mtmt) cc_final: 0.8877 (mtmm) REVERT: B 121 PHE cc_start: 0.8439 (m-80) cc_final: 0.8168 (m-80) REVERT: B 163 GLN cc_start: 0.8676 (tt0) cc_final: 0.7983 (tp-100) REVERT: B 186 TYR cc_start: 0.8752 (m-10) cc_final: 0.8539 (m-80) REVERT: B 193 PHE cc_start: 0.8487 (m-80) cc_final: 0.8237 (m-80) REVERT: B 195 MET cc_start: 0.8267 (mtp) cc_final: 0.7949 (ttt) REVERT: B 271 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 289 MET cc_start: 0.7058 (ttm) cc_final: 0.6817 (ttm) REVERT: B 319 LYS cc_start: 0.8967 (mttm) cc_final: 0.8678 (mttm) REVERT: A 49 MET cc_start: 0.7862 (mmm) cc_final: 0.6974 (ppp) REVERT: A 119 ASN cc_start: 0.8981 (m-40) cc_final: 0.8460 (t0) REVERT: A 219 GLU cc_start: 0.8970 (tp30) cc_final: 0.8663 (mm-30) REVERT: A 327 LEU cc_start: 0.9184 (tp) cc_final: 0.8980 (tt) REVERT: A 520 MET cc_start: 0.8618 (mmm) cc_final: 0.8288 (mmm) REVERT: A 577 ASP cc_start: 0.9119 (p0) cc_final: 0.8881 (t70) outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 58.4535 time to fit residues: 18494.4391 Evaluate side-chains 228 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 206 GLN B 210 ASN A 86 GLN A 101 ASN A 117 GLN A 135 ASN A 202 ASN A 336 GLN A 429 ASN A 479 ASN A 564 GLN A 593 GLN A 633 ASN A 661 HIS ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9221 Z= 0.189 Angle : 0.625 11.273 12491 Z= 0.331 Chirality : 0.040 0.130 1388 Planarity : 0.004 0.061 1546 Dihedral : 5.069 27.336 1204 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.61 % Allowed : 4.78 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1073 helix: 0.53 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.73 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 123 HIS 0.007 0.001 HIS A 122 PHE 0.049 0.002 PHE B 152 TYR 0.020 0.001 TYR C 44 ARG 0.006 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 302 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8499 (t60) cc_final: 0.8246 (t60) REVERT: C 44 TYR cc_start: 0.7238 (t80) cc_final: 0.6619 (t80) REVERT: C 45 ASP cc_start: 0.7904 (p0) cc_final: 0.7315 (p0) REVERT: C 80 HIS cc_start: 0.8607 (m90) cc_final: 0.7910 (m90) REVERT: C 96 TRP cc_start: 0.4950 (m-10) cc_final: 0.4466 (m-10) REVERT: C 99 PHE cc_start: 0.8680 (m-80) cc_final: 0.8397 (m-10) REVERT: C 171 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6977 (mt-10) REVERT: C 176 PHE cc_start: 0.7833 (p90) cc_final: 0.7470 (p90) REVERT: C 177 MET cc_start: 0.8541 (tmm) cc_final: 0.8236 (tmm) REVERT: C 184 TYR cc_start: 0.8616 (t80) cc_final: 0.8329 (t80) REVERT: B 5 ASN cc_start: 0.7493 (p0) cc_final: 0.6840 (t0) REVERT: B 37 GLN cc_start: 0.9040 (tt0) cc_final: 0.8697 (tm-30) REVERT: B 61 LEU cc_start: 0.9501 (mt) cc_final: 0.9111 (tt) REVERT: B 64 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8871 (tm-30) REVERT: B 92 ASN cc_start: 0.8335 (m-40) cc_final: 0.8110 (m-40) REVERT: B 106 PHE cc_start: 0.8199 (m-80) cc_final: 0.7487 (p90) REVERT: B 119 LYS cc_start: 0.9488 (mtmt) cc_final: 0.9151 (mtmm) REVERT: B 121 PHE cc_start: 0.8379 (m-80) cc_final: 0.8032 (m-80) REVERT: B 163 GLN cc_start: 0.8557 (tt0) cc_final: 0.7856 (tp-100) REVERT: B 191 MET cc_start: 0.8899 (tmm) cc_final: 0.8497 (tmm) REVERT: B 274 ILE cc_start: 0.9305 (mt) cc_final: 0.9088 (tt) REVERT: B 286 HIS cc_start: 0.7725 (m-70) cc_final: 0.7276 (m-70) REVERT: B 289 MET cc_start: 0.6771 (ttm) cc_final: 0.6396 (ttm) REVERT: B 319 LYS cc_start: 0.8979 (mttm) cc_final: 0.8753 (mttm) REVERT: A 49 MET cc_start: 0.7681 (mmm) cc_final: 0.6778 (ppp) REVERT: A 219 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 327 LEU cc_start: 0.9163 (tp) cc_final: 0.8926 (tt) REVERT: A 388 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8624 (mmtm) REVERT: A 402 LEU cc_start: 0.9341 (tt) cc_final: 0.9059 (tt) REVERT: A 438 MET cc_start: 0.8845 (mmp) cc_final: 0.8369 (mmm) REVERT: A 472 LEU cc_start: 0.9409 (mt) cc_final: 0.9021 (mm) REVERT: A 481 PHE cc_start: 0.7762 (t80) cc_final: 0.7489 (t80) REVERT: A 520 MET cc_start: 0.8477 (mmm) cc_final: 0.8126 (mmm) REVERT: A 577 ASP cc_start: 0.9146 (p0) cc_final: 0.8642 (t70) outliers start: 6 outliers final: 1 residues processed: 305 average time/residue: 0.1921 time to fit residues: 81.1708 Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.0170 chunk 33 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 479 ASN A 633 ASN A 663 HIS ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9221 Z= 0.167 Angle : 0.585 10.242 12491 Z= 0.307 Chirality : 0.038 0.128 1388 Planarity : 0.004 0.058 1546 Dihedral : 4.671 23.989 1204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1073 helix: 1.44 (0.17), residues: 831 sheet: None (None), residues: 0 loop : -2.59 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 68 HIS 0.004 0.001 HIS A 661 PHE 0.038 0.001 PHE B 152 TYR 0.017 0.001 TYR B 186 ARG 0.005 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8433 (t60) cc_final: 0.8092 (t60) REVERT: C 45 ASP cc_start: 0.7817 (p0) cc_final: 0.7345 (p0) REVERT: C 80 HIS cc_start: 0.8626 (m90) cc_final: 0.8120 (m90) REVERT: C 81 LEU cc_start: 0.9317 (mt) cc_final: 0.8926 (mt) REVERT: C 85 GLU cc_start: 0.8443 (tp30) cc_final: 0.7652 (pt0) REVERT: C 91 ARG cc_start: 0.6401 (mtt90) cc_final: 0.3962 (ptm160) REVERT: C 99 PHE cc_start: 0.8594 (m-80) cc_final: 0.8291 (m-10) REVERT: C 176 PHE cc_start: 0.7928 (p90) cc_final: 0.7475 (p90) REVERT: C 184 TYR cc_start: 0.8623 (t80) cc_final: 0.8340 (t80) REVERT: B 5 ASN cc_start: 0.7425 (p0) cc_final: 0.6843 (t0) REVERT: B 37 GLN cc_start: 0.8937 (tt0) cc_final: 0.8543 (tm-30) REVERT: B 106 PHE cc_start: 0.8287 (m-80) cc_final: 0.7554 (p90) REVERT: B 114 LEU cc_start: 0.9166 (tp) cc_final: 0.8615 (tp) REVERT: B 118 LEU cc_start: 0.9169 (mm) cc_final: 0.8943 (mm) REVERT: B 119 LYS cc_start: 0.9533 (mtmt) cc_final: 0.9170 (mtmm) REVERT: B 121 PHE cc_start: 0.8410 (m-80) cc_final: 0.8132 (m-80) REVERT: B 137 ASN cc_start: 0.6796 (m-40) cc_final: 0.6522 (t0) REVERT: B 152 PHE cc_start: 0.7394 (m-80) cc_final: 0.7194 (m-80) REVERT: B 163 GLN cc_start: 0.8533 (tt0) cc_final: 0.7773 (tp-100) REVERT: B 191 MET cc_start: 0.8772 (tmm) cc_final: 0.8515 (tmm) REVERT: B 274 ILE cc_start: 0.9337 (mt) cc_final: 0.8933 (tt) REVERT: B 286 HIS cc_start: 0.7403 (m-70) cc_final: 0.7162 (m-70) REVERT: B 289 MET cc_start: 0.6652 (ttm) cc_final: 0.6319 (ttm) REVERT: B 319 LYS cc_start: 0.9076 (mttm) cc_final: 0.8851 (mttm) REVERT: A 49 MET cc_start: 0.7145 (mmm) cc_final: 0.6758 (ppp) REVERT: A 69 ASN cc_start: 0.9058 (m110) cc_final: 0.8751 (t0) REVERT: A 219 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8458 (mm-30) REVERT: A 327 LEU cc_start: 0.9133 (tp) cc_final: 0.8830 (pp) REVERT: A 379 MET cc_start: 0.8171 (tpp) cc_final: 0.7866 (tpp) REVERT: A 388 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8621 (mmtm) REVERT: A 438 MET cc_start: 0.8962 (mmp) cc_final: 0.8579 (mmm) REVERT: A 441 MET cc_start: 0.8135 (mtm) cc_final: 0.7837 (mtt) REVERT: A 481 PHE cc_start: 0.7842 (t80) cc_final: 0.7442 (t80) REVERT: A 520 MET cc_start: 0.8273 (mmm) cc_final: 0.7958 (mmm) REVERT: A 577 ASP cc_start: 0.9066 (p0) cc_final: 0.8597 (t70) REVERT: A 675 LYS cc_start: 0.8406 (tttt) cc_final: 0.7939 (tptm) outliers start: 2 outliers final: 1 residues processed: 306 average time/residue: 0.1972 time to fit residues: 84.8880 Evaluate side-chains 228 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9221 Z= 0.180 Angle : 0.591 10.323 12491 Z= 0.310 Chirality : 0.039 0.210 1388 Planarity : 0.004 0.056 1546 Dihedral : 4.565 22.415 1204 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.22 (0.25), residues: 1073 helix: 1.70 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.50 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 541 HIS 0.005 0.001 HIS C 180 PHE 0.032 0.001 PHE B 152 TYR 0.028 0.001 TYR C 44 ARG 0.007 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8463 (t60) cc_final: 0.8142 (t60) REVERT: C 45 ASP cc_start: 0.7775 (p0) cc_final: 0.7158 (p0) REVERT: C 80 HIS cc_start: 0.8627 (m90) cc_final: 0.8096 (m90) REVERT: C 81 LEU cc_start: 0.9289 (mt) cc_final: 0.8532 (pp) REVERT: C 85 GLU cc_start: 0.8488 (tp30) cc_final: 0.7569 (pt0) REVERT: C 91 ARG cc_start: 0.6421 (mtt90) cc_final: 0.4131 (ptm160) REVERT: C 96 TRP cc_start: 0.4906 (m-10) cc_final: 0.4526 (m-10) REVERT: C 99 PHE cc_start: 0.8616 (m-80) cc_final: 0.8291 (m-10) REVERT: C 104 ILE cc_start: 0.8800 (tp) cc_final: 0.8465 (pt) REVERT: C 112 GLU cc_start: 0.8123 (tp30) cc_final: 0.7917 (tm-30) REVERT: C 176 PHE cc_start: 0.7829 (p90) cc_final: 0.7336 (p90) REVERT: C 177 MET cc_start: 0.8629 (tmm) cc_final: 0.8403 (tmm) REVERT: C 184 TYR cc_start: 0.8594 (t80) cc_final: 0.8146 (t80) REVERT: B 5 ASN cc_start: 0.7418 (p0) cc_final: 0.5507 (t0) REVERT: B 9 GLN cc_start: 0.8405 (mt0) cc_final: 0.7914 (mt0) REVERT: B 37 GLN cc_start: 0.8933 (tt0) cc_final: 0.8596 (tm-30) REVERT: B 64 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8914 (tm-30) REVERT: B 79 HIS cc_start: 0.8193 (m90) cc_final: 0.7801 (m90) REVERT: B 95 PHE cc_start: 0.8166 (t80) cc_final: 0.7941 (t80) REVERT: B 106 PHE cc_start: 0.8289 (m-80) cc_final: 0.7562 (p90) REVERT: B 114 LEU cc_start: 0.9148 (tp) cc_final: 0.8477 (tp) REVERT: B 115 LEU cc_start: 0.9504 (tp) cc_final: 0.9233 (tp) REVERT: B 119 LYS cc_start: 0.9537 (mtmt) cc_final: 0.9172 (mtmm) REVERT: B 121 PHE cc_start: 0.8259 (m-80) cc_final: 0.8001 (m-80) REVERT: B 123 TRP cc_start: 0.7160 (m100) cc_final: 0.6927 (m100) REVERT: B 163 GLN cc_start: 0.8373 (tt0) cc_final: 0.7931 (tp-100) REVERT: B 191 MET cc_start: 0.8674 (tmm) cc_final: 0.8378 (tmm) REVERT: B 193 PHE cc_start: 0.8293 (m-80) cc_final: 0.7753 (m-80) REVERT: B 289 MET cc_start: 0.6612 (ttm) cc_final: 0.6293 (ttm) REVERT: B 319 LYS cc_start: 0.9059 (mttm) cc_final: 0.8835 (mttm) REVERT: A 49 MET cc_start: 0.7265 (mmm) cc_final: 0.6645 (ppp) REVERT: A 69 ASN cc_start: 0.9063 (m110) cc_final: 0.8784 (t0) REVERT: A 109 LEU cc_start: 0.9388 (tp) cc_final: 0.9064 (tp) REVERT: A 152 MET cc_start: 0.8474 (mmm) cc_final: 0.7727 (tpt) REVERT: A 176 LEU cc_start: 0.9009 (mm) cc_final: 0.8786 (pp) REVERT: A 219 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 327 LEU cc_start: 0.9138 (tp) cc_final: 0.8817 (pp) REVERT: A 388 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8525 (mmtm) REVERT: A 441 MET cc_start: 0.8019 (mtm) cc_final: 0.7542 (mtm) REVERT: A 481 PHE cc_start: 0.7883 (t80) cc_final: 0.7369 (t80) REVERT: A 577 ASP cc_start: 0.9015 (p0) cc_final: 0.8559 (t70) REVERT: A 675 LYS cc_start: 0.8420 (tttt) cc_final: 0.7945 (tptm) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1782 time to fit residues: 71.0290 Evaluate side-chains 232 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 HIS B 175 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9221 Z= 0.219 Angle : 0.621 10.138 12491 Z= 0.329 Chirality : 0.039 0.134 1388 Planarity : 0.004 0.057 1546 Dihedral : 4.636 22.342 1204 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.23 (0.25), residues: 1073 helix: 1.69 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 541 HIS 0.004 0.001 HIS A 113 PHE 0.056 0.002 PHE B 152 TYR 0.021 0.001 TYR C 44 ARG 0.006 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8422 (t60) cc_final: 0.8125 (t60) REVERT: C 45 ASP cc_start: 0.7557 (p0) cc_final: 0.7090 (p0) REVERT: C 80 HIS cc_start: 0.8667 (m90) cc_final: 0.8191 (m90) REVERT: C 81 LEU cc_start: 0.9316 (mt) cc_final: 0.9008 (mt) REVERT: C 85 GLU cc_start: 0.8554 (tp30) cc_final: 0.7513 (pt0) REVERT: C 91 ARG cc_start: 0.6473 (mtt90) cc_final: 0.4102 (ptm160) REVERT: C 99 PHE cc_start: 0.8542 (m-80) cc_final: 0.8196 (m-10) REVERT: C 104 ILE cc_start: 0.8846 (tp) cc_final: 0.8503 (pt) REVERT: C 176 PHE cc_start: 0.8014 (p90) cc_final: 0.7514 (p90) REVERT: C 177 MET cc_start: 0.8537 (tmm) cc_final: 0.8241 (tmm) REVERT: C 184 TYR cc_start: 0.8742 (t80) cc_final: 0.8402 (t80) REVERT: B 5 ASN cc_start: 0.7290 (p0) cc_final: 0.5233 (t0) REVERT: B 9 GLN cc_start: 0.8349 (mt0) cc_final: 0.8022 (mt0) REVERT: B 37 GLN cc_start: 0.8867 (tt0) cc_final: 0.8512 (tm-30) REVERT: B 64 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8869 (tm-30) REVERT: B 106 PHE cc_start: 0.8288 (m-80) cc_final: 0.7527 (p90) REVERT: B 114 LEU cc_start: 0.9193 (tp) cc_final: 0.8543 (tp) REVERT: B 115 LEU cc_start: 0.9571 (tp) cc_final: 0.9356 (tp) REVERT: B 119 LYS cc_start: 0.9554 (mtmt) cc_final: 0.9024 (mtmm) REVERT: B 121 PHE cc_start: 0.8384 (m-80) cc_final: 0.8103 (m-80) REVERT: B 152 PHE cc_start: 0.7224 (m-80) cc_final: 0.6775 (m-80) REVERT: B 163 GLN cc_start: 0.8464 (tt0) cc_final: 0.8029 (tp-100) REVERT: B 191 MET cc_start: 0.8667 (tmm) cc_final: 0.8315 (tmm) REVERT: B 193 PHE cc_start: 0.8512 (m-80) cc_final: 0.8062 (m-80) REVERT: B 274 ILE cc_start: 0.9329 (mt) cc_final: 0.8898 (tt) REVERT: B 289 MET cc_start: 0.6724 (ttm) cc_final: 0.6487 (ttm) REVERT: B 319 LYS cc_start: 0.9036 (mttm) cc_final: 0.8814 (mttm) REVERT: A 49 MET cc_start: 0.7351 (mmm) cc_final: 0.6621 (ppp) REVERT: A 69 ASN cc_start: 0.9104 (m110) cc_final: 0.8815 (t0) REVERT: A 219 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8428 (mm-30) REVERT: A 327 LEU cc_start: 0.9183 (tp) cc_final: 0.8872 (pp) REVERT: A 329 ASP cc_start: 0.8165 (t0) cc_final: 0.7961 (t0) REVERT: A 388 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8567 (mmtm) REVERT: A 438 MET cc_start: 0.8792 (mmp) cc_final: 0.8568 (mmm) REVERT: A 481 PHE cc_start: 0.7883 (t80) cc_final: 0.7320 (t80) REVERT: A 577 ASP cc_start: 0.8981 (p0) cc_final: 0.8664 (t70) REVERT: A 675 LYS cc_start: 0.8303 (tttt) cc_final: 0.7685 (tptm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1717 time to fit residues: 67.3156 Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN B 47 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9221 Z= 0.175 Angle : 0.612 9.575 12491 Z= 0.316 Chirality : 0.039 0.136 1388 Planarity : 0.004 0.055 1546 Dihedral : 4.590 20.924 1204 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.43 (0.26), residues: 1073 helix: 1.83 (0.17), residues: 833 sheet: None (None), residues: 0 loop : -2.35 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 541 HIS 0.005 0.001 HIS C 180 PHE 0.045 0.001 PHE B 152 TYR 0.038 0.001 TYR C 44 ARG 0.006 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8415 (t60) cc_final: 0.8082 (t60) REVERT: C 45 ASP cc_start: 0.7762 (p0) cc_final: 0.7195 (p0) REVERT: C 80 HIS cc_start: 0.8700 (m90) cc_final: 0.8329 (m90) REVERT: C 81 LEU cc_start: 0.9274 (mt) cc_final: 0.8478 (pp) REVERT: C 85 GLU cc_start: 0.8631 (tp30) cc_final: 0.7587 (pt0) REVERT: C 91 ARG cc_start: 0.6446 (mtt90) cc_final: 0.4090 (ptm160) REVERT: C 96 TRP cc_start: 0.4844 (m-10) cc_final: 0.4443 (m-10) REVERT: C 99 PHE cc_start: 0.8569 (m-80) cc_final: 0.8227 (m-10) REVERT: C 104 ILE cc_start: 0.8817 (tp) cc_final: 0.8469 (pt) REVERT: C 176 PHE cc_start: 0.7989 (p90) cc_final: 0.7521 (p90) REVERT: C 177 MET cc_start: 0.8566 (tmm) cc_final: 0.8226 (tmm) REVERT: B 5 ASN cc_start: 0.7277 (p0) cc_final: 0.5226 (t0) REVERT: B 9 GLN cc_start: 0.8367 (mt0) cc_final: 0.8023 (mt0) REVERT: B 37 GLN cc_start: 0.8848 (tt0) cc_final: 0.8509 (tm-30) REVERT: B 64 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8810 (tm-30) REVERT: B 80 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8883 (pt0) REVERT: B 92 ASN cc_start: 0.8682 (m-40) cc_final: 0.8414 (m-40) REVERT: B 106 PHE cc_start: 0.8263 (m-80) cc_final: 0.7594 (p90) REVERT: B 114 LEU cc_start: 0.9171 (tp) cc_final: 0.8532 (tp) REVERT: B 115 LEU cc_start: 0.9566 (tp) cc_final: 0.9265 (tp) REVERT: B 119 LYS cc_start: 0.9543 (mtmt) cc_final: 0.9028 (mtmm) REVERT: B 121 PHE cc_start: 0.8302 (m-80) cc_final: 0.8019 (m-80) REVERT: B 152 PHE cc_start: 0.7104 (m-80) cc_final: 0.6797 (m-80) REVERT: B 163 GLN cc_start: 0.8450 (tt0) cc_final: 0.7974 (tp-100) REVERT: B 191 MET cc_start: 0.8574 (tmm) cc_final: 0.8350 (tmm) REVERT: B 193 PHE cc_start: 0.8300 (m-80) cc_final: 0.7998 (m-80) REVERT: B 211 PHE cc_start: 0.7960 (t80) cc_final: 0.7523 (t80) REVERT: B 289 MET cc_start: 0.6768 (ttm) cc_final: 0.6525 (ttm) REVERT: B 319 LYS cc_start: 0.8909 (mttm) cc_final: 0.8694 (mttm) REVERT: A 39 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8622 (ptpp) REVERT: A 49 MET cc_start: 0.7424 (mmm) cc_final: 0.6693 (ppp) REVERT: A 69 ASN cc_start: 0.9061 (m110) cc_final: 0.8799 (t0) REVERT: A 219 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 327 LEU cc_start: 0.9118 (tp) cc_final: 0.8778 (pp) REVERT: A 329 ASP cc_start: 0.7989 (t0) cc_final: 0.7736 (t0) REVERT: A 374 GLN cc_start: 0.8918 (mt0) cc_final: 0.8177 (mm-40) REVERT: A 388 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8514 (mmtm) REVERT: A 434 ILE cc_start: 0.9335 (mt) cc_final: 0.9092 (mt) REVERT: A 438 MET cc_start: 0.8695 (mmp) cc_final: 0.8489 (mmm) REVERT: A 481 PHE cc_start: 0.7884 (t80) cc_final: 0.7457 (t80) REVERT: A 577 ASP cc_start: 0.8949 (p0) cc_final: 0.8655 (t70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1754 time to fit residues: 70.4255 Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9221 Z= 0.258 Angle : 0.666 10.435 12491 Z= 0.347 Chirality : 0.042 0.158 1388 Planarity : 0.004 0.058 1546 Dihedral : 4.843 21.902 1204 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.10 (0.25), residues: 1073 helix: 1.57 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.32 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 541 HIS 0.004 0.001 HIS C 180 PHE 0.036 0.002 PHE B 152 TYR 0.047 0.002 TYR C 44 ARG 0.008 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8377 (t60) cc_final: 0.8099 (t60) REVERT: C 45 ASP cc_start: 0.7701 (p0) cc_final: 0.7379 (p0) REVERT: C 80 HIS cc_start: 0.8758 (m90) cc_final: 0.8350 (m90) REVERT: C 85 GLU cc_start: 0.8699 (tp30) cc_final: 0.8293 (tp30) REVERT: C 91 ARG cc_start: 0.6553 (mtt90) cc_final: 0.4193 (ptm160) REVERT: C 96 TRP cc_start: 0.5006 (m-10) cc_final: 0.4563 (m-10) REVERT: C 99 PHE cc_start: 0.8578 (m-80) cc_final: 0.8193 (m-10) REVERT: C 104 ILE cc_start: 0.8828 (tp) cc_final: 0.8524 (pt) REVERT: C 176 PHE cc_start: 0.7920 (p90) cc_final: 0.7484 (p90) REVERT: C 177 MET cc_start: 0.8552 (tmm) cc_final: 0.8230 (tmm) REVERT: B 9 GLN cc_start: 0.8343 (mt0) cc_final: 0.8098 (mt0) REVERT: B 37 GLN cc_start: 0.8906 (tt0) cc_final: 0.8599 (tt0) REVERT: B 64 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8856 (tm-30) REVERT: B 80 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8983 (pt0) REVERT: B 92 ASN cc_start: 0.8618 (m-40) cc_final: 0.8381 (m-40) REVERT: B 106 PHE cc_start: 0.8252 (m-80) cc_final: 0.7500 (p90) REVERT: B 114 LEU cc_start: 0.9184 (tp) cc_final: 0.8615 (tp) REVERT: B 118 LEU cc_start: 0.9206 (mm) cc_final: 0.8956 (mm) REVERT: B 119 LYS cc_start: 0.9487 (mtmt) cc_final: 0.9178 (mtmm) REVERT: B 121 PHE cc_start: 0.8432 (m-80) cc_final: 0.8232 (m-80) REVERT: B 152 PHE cc_start: 0.7181 (m-80) cc_final: 0.6929 (m-80) REVERT: B 163 GLN cc_start: 0.8538 (tt0) cc_final: 0.8005 (tp-100) REVERT: B 191 MET cc_start: 0.8580 (tmm) cc_final: 0.8151 (tmm) REVERT: B 193 PHE cc_start: 0.8450 (m-80) cc_final: 0.8156 (m-80) REVERT: B 195 MET cc_start: 0.8274 (ttp) cc_final: 0.7795 (mtp) REVERT: B 211 PHE cc_start: 0.7878 (t80) cc_final: 0.7424 (t80) REVERT: A 49 MET cc_start: 0.7324 (mmm) cc_final: 0.6812 (ppp) REVERT: A 69 ASN cc_start: 0.9126 (m110) cc_final: 0.8829 (t0) REVERT: A 219 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 327 LEU cc_start: 0.9184 (tp) cc_final: 0.8953 (tt) REVERT: A 329 ASP cc_start: 0.8181 (t0) cc_final: 0.7912 (t0) REVERT: A 388 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8566 (mmtm) REVERT: A 481 PHE cc_start: 0.7987 (t80) cc_final: 0.7660 (t80) REVERT: A 577 ASP cc_start: 0.8944 (p0) cc_final: 0.8662 (t70) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1685 time to fit residues: 65.1826 Evaluate side-chains 223 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9221 Z= 0.207 Angle : 0.641 10.494 12491 Z= 0.335 Chirality : 0.040 0.146 1388 Planarity : 0.004 0.059 1546 Dihedral : 4.706 21.922 1204 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.25 (0.26), residues: 1073 helix: 1.69 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.32 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 541 HIS 0.008 0.001 HIS C 123 PHE 0.031 0.001 PHE B 152 TYR 0.046 0.002 TYR C 44 ARG 0.007 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8396 (t60) cc_final: 0.8132 (t60) REVERT: C 73 ASN cc_start: 0.8233 (m-40) cc_final: 0.8032 (m-40) REVERT: C 80 HIS cc_start: 0.8782 (m90) cc_final: 0.8362 (m90) REVERT: C 81 LEU cc_start: 0.9313 (mt) cc_final: 0.8870 (pp) REVERT: C 85 GLU cc_start: 0.8697 (tp30) cc_final: 0.8241 (tp30) REVERT: C 91 ARG cc_start: 0.6547 (mtt90) cc_final: 0.4150 (ptm160) REVERT: C 96 TRP cc_start: 0.5063 (m-10) cc_final: 0.4617 (m-10) REVERT: C 99 PHE cc_start: 0.8570 (m-80) cc_final: 0.8176 (m-10) REVERT: C 104 ILE cc_start: 0.8819 (tp) cc_final: 0.8511 (pt) REVERT: C 176 PHE cc_start: 0.8015 (p90) cc_final: 0.7701 (p90) REVERT: C 177 MET cc_start: 0.8530 (tmm) cc_final: 0.8169 (tmm) REVERT: B 5 ASN cc_start: 0.7614 (p0) cc_final: 0.6919 (p0) REVERT: B 9 GLN cc_start: 0.8389 (mt0) cc_final: 0.8172 (mt0) REVERT: B 37 GLN cc_start: 0.8826 (tt0) cc_final: 0.8610 (tt0) REVERT: B 63 TRP cc_start: 0.8034 (t60) cc_final: 0.7778 (t60) REVERT: B 80 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8939 (pt0) REVERT: B 92 ASN cc_start: 0.8587 (m-40) cc_final: 0.8369 (m-40) REVERT: B 106 PHE cc_start: 0.8224 (m-80) cc_final: 0.7487 (p90) REVERT: B 114 LEU cc_start: 0.9156 (tp) cc_final: 0.8466 (tp) REVERT: B 115 LEU cc_start: 0.9625 (tp) cc_final: 0.9417 (tp) REVERT: B 118 LEU cc_start: 0.9192 (mm) cc_final: 0.8959 (mm) REVERT: B 119 LYS cc_start: 0.9421 (mtmt) cc_final: 0.8932 (mtmm) REVERT: B 152 PHE cc_start: 0.7107 (m-80) cc_final: 0.6825 (m-80) REVERT: B 163 GLN cc_start: 0.8485 (tt0) cc_final: 0.7923 (tp-100) REVERT: B 193 PHE cc_start: 0.8427 (m-80) cc_final: 0.8163 (m-80) REVERT: B 319 LYS cc_start: 0.9426 (mtmm) cc_final: 0.8948 (mmmt) REVERT: A 39 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8573 (ptpp) REVERT: A 69 ASN cc_start: 0.9101 (m110) cc_final: 0.8757 (t0) REVERT: A 219 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 327 LEU cc_start: 0.9157 (tp) cc_final: 0.8803 (pp) REVERT: A 374 GLN cc_start: 0.8901 (mt0) cc_final: 0.8237 (mm-40) REVERT: A 388 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8558 (mmtm) REVERT: A 481 PHE cc_start: 0.7994 (t80) cc_final: 0.7607 (t80) REVERT: A 577 ASP cc_start: 0.8924 (p0) cc_final: 0.8633 (t70) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1698 time to fit residues: 66.2451 Evaluate side-chains 228 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9221 Z= 0.185 Angle : 0.630 10.377 12491 Z= 0.326 Chirality : 0.040 0.149 1388 Planarity : 0.004 0.060 1546 Dihedral : 4.647 20.371 1204 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.41 (0.26), residues: 1073 helix: 1.79 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -2.25 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 541 HIS 0.004 0.001 HIS C 123 PHE 0.029 0.001 PHE B 152 TYR 0.023 0.001 TYR C 44 ARG 0.008 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8370 (t60) cc_final: 0.8122 (t60) REVERT: C 80 HIS cc_start: 0.8777 (m90) cc_final: 0.8355 (m90) REVERT: C 81 LEU cc_start: 0.9280 (mt) cc_final: 0.8876 (pp) REVERT: C 85 GLU cc_start: 0.8865 (tp30) cc_final: 0.8328 (tp30) REVERT: C 91 ARG cc_start: 0.6032 (mtt90) cc_final: 0.4116 (ptm160) REVERT: C 96 TRP cc_start: 0.5068 (m-10) cc_final: 0.4646 (m-10) REVERT: C 99 PHE cc_start: 0.8529 (m-80) cc_final: 0.8125 (m-10) REVERT: C 104 ILE cc_start: 0.8809 (tp) cc_final: 0.8490 (pt) REVERT: C 176 PHE cc_start: 0.8054 (p90) cc_final: 0.7748 (p90) REVERT: C 177 MET cc_start: 0.8561 (tmm) cc_final: 0.8212 (tmm) REVERT: B 5 ASN cc_start: 0.7627 (p0) cc_final: 0.6896 (p0) REVERT: B 9 GLN cc_start: 0.8399 (mt0) cc_final: 0.8163 (mt0) REVERT: B 37 GLN cc_start: 0.8882 (tt0) cc_final: 0.8628 (tt0) REVERT: B 92 ASN cc_start: 0.8626 (m-40) cc_final: 0.8402 (m-40) REVERT: B 106 PHE cc_start: 0.8257 (m-80) cc_final: 0.7663 (p90) REVERT: B 114 LEU cc_start: 0.9166 (tp) cc_final: 0.8497 (tp) REVERT: B 115 LEU cc_start: 0.9590 (tp) cc_final: 0.9282 (tp) REVERT: B 119 LYS cc_start: 0.9427 (mtmt) cc_final: 0.8902 (mtmm) REVERT: B 152 PHE cc_start: 0.6968 (m-80) cc_final: 0.6542 (m-80) REVERT: B 163 GLN cc_start: 0.8432 (tt0) cc_final: 0.7899 (tp-100) REVERT: B 193 PHE cc_start: 0.8438 (m-80) cc_final: 0.8144 (m-80) REVERT: B 195 MET cc_start: 0.8176 (ttp) cc_final: 0.7704 (mtp) REVERT: B 269 MET cc_start: 0.8450 (ttp) cc_final: 0.8162 (tmm) REVERT: B 319 LYS cc_start: 0.9425 (mtmm) cc_final: 0.8973 (mmmt) REVERT: A 39 LYS cc_start: 0.8890 (ptpp) cc_final: 0.8604 (ptpp) REVERT: A 69 ASN cc_start: 0.9037 (m110) cc_final: 0.8714 (t0) REVERT: A 219 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 327 LEU cc_start: 0.9126 (tp) cc_final: 0.8775 (pp) REVERT: A 374 GLN cc_start: 0.8918 (mt0) cc_final: 0.8225 (mm-40) REVERT: A 388 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8587 (mmtm) REVERT: A 481 PHE cc_start: 0.8056 (t80) cc_final: 0.7597 (t80) REVERT: A 552 GLU cc_start: 0.8883 (pp20) cc_final: 0.8479 (pp20) REVERT: A 577 ASP cc_start: 0.8908 (p0) cc_final: 0.8621 (t70) REVERT: A 619 TYR cc_start: 0.9126 (m-80) cc_final: 0.8834 (m-80) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1704 time to fit residues: 67.8588 Evaluate side-chains 229 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.0270 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS B 323 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN A 595 ASN A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9221 Z= 0.163 Angle : 0.630 10.430 12491 Z= 0.320 Chirality : 0.040 0.148 1388 Planarity : 0.004 0.060 1546 Dihedral : 4.521 20.083 1204 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.70 (0.26), residues: 1073 helix: 2.04 (0.18), residues: 827 sheet: None (None), residues: 0 loop : -2.20 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 541 HIS 0.010 0.001 HIS B 286 PHE 0.027 0.001 PHE B 152 TYR 0.046 0.001 TYR C 44 ARG 0.010 0.000 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8378 (t60) cc_final: 0.8137 (t60) REVERT: C 80 HIS cc_start: 0.8769 (m90) cc_final: 0.8317 (m90) REVERT: C 81 LEU cc_start: 0.9263 (mt) cc_final: 0.8843 (pp) REVERT: C 85 GLU cc_start: 0.8830 (tp30) cc_final: 0.8281 (tp30) REVERT: C 91 ARG cc_start: 0.6228 (mtt90) cc_final: 0.4256 (ptm160) REVERT: C 96 TRP cc_start: 0.4851 (m-10) cc_final: 0.4434 (m-10) REVERT: C 99 PHE cc_start: 0.8534 (m-80) cc_final: 0.8127 (m-10) REVERT: C 104 ILE cc_start: 0.8797 (tp) cc_final: 0.8468 (pt) REVERT: C 171 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5739 (tt0) REVERT: C 176 PHE cc_start: 0.8127 (p90) cc_final: 0.7827 (p90) REVERT: C 177 MET cc_start: 0.8592 (tmm) cc_final: 0.8211 (tmm) REVERT: B 5 ASN cc_start: 0.7732 (p0) cc_final: 0.6968 (p0) REVERT: B 9 GLN cc_start: 0.8386 (mt0) cc_final: 0.8154 (mt0) REVERT: B 37 GLN cc_start: 0.8902 (tt0) cc_final: 0.8701 (tt0) REVERT: B 63 TRP cc_start: 0.8056 (t60) cc_final: 0.7670 (t60) REVERT: B 92 ASN cc_start: 0.8665 (m-40) cc_final: 0.8370 (m-40) REVERT: B 106 PHE cc_start: 0.8146 (m-80) cc_final: 0.7503 (p90) REVERT: B 114 LEU cc_start: 0.9148 (tp) cc_final: 0.8634 (tp) REVERT: B 115 LEU cc_start: 0.9572 (tp) cc_final: 0.9277 (tp) REVERT: B 117 TYR cc_start: 0.8446 (m-10) cc_final: 0.7973 (m-10) REVERT: B 119 LYS cc_start: 0.9390 (mtmt) cc_final: 0.8865 (mtmm) REVERT: B 152 PHE cc_start: 0.6725 (m-80) cc_final: 0.6251 (m-80) REVERT: B 163 GLN cc_start: 0.8341 (tt0) cc_final: 0.7906 (tp-100) REVERT: B 175 ASN cc_start: 0.8837 (m-40) cc_final: 0.8630 (m-40) REVERT: B 193 PHE cc_start: 0.8365 (m-80) cc_final: 0.8074 (m-80) REVERT: B 195 MET cc_start: 0.8208 (ttp) cc_final: 0.7659 (mtp) REVERT: B 269 MET cc_start: 0.8426 (ttp) cc_final: 0.8057 (tmm) REVERT: B 319 LYS cc_start: 0.9386 (mtmm) cc_final: 0.8954 (mmmt) REVERT: A 69 ASN cc_start: 0.8979 (m110) cc_final: 0.8730 (t0) REVERT: A 219 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 327 LEU cc_start: 0.9092 (tp) cc_final: 0.8746 (pp) REVERT: A 374 GLN cc_start: 0.8848 (mt0) cc_final: 0.8107 (mm-40) REVERT: A 388 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8562 (mmtm) REVERT: A 481 PHE cc_start: 0.7845 (t80) cc_final: 0.7380 (t80) REVERT: A 552 GLU cc_start: 0.8821 (pp20) cc_final: 0.8533 (pp20) REVERT: A 577 ASP cc_start: 0.8953 (p0) cc_final: 0.8533 (t70) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1745 time to fit residues: 70.8550 Evaluate side-chains 236 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN B 47 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** D 745 HIS ** 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 = 0.3719 r_free = 0.3719 target = 0.113440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084780 restraints weight = 28136.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087069 restraints weight = 17088.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088629 restraints weight = 12117.014| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9221 Z= 0.204 Angle : 0.654 10.671 12491 Z= 0.338 Chirality : 0.041 0.147 1388 Planarity : 0.004 0.060 1546 Dihedral : 4.567 19.510 1204 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.44 (0.26), residues: 1073 helix: 1.79 (0.18), residues: 835 sheet: None (None), residues: 0 loop : -2.19 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 115 HIS 0.003 0.001 HIS C 180 PHE 0.024 0.001 PHE B 152 TYR 0.044 0.002 TYR C 44 ARG 0.009 0.000 ARG C 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.15 seconds wall clock time: 342 minutes 56.85 seconds (20576.85 seconds total)