Starting phenix.real_space_refine on Tue Feb 13 12:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de3_27383/02_2024/8de3_27383.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 4100 2.51 5 N 957 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6199 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4298 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} Chain breaks: 1 Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Unusual residues: {' CL': 1, ' NA': 2, 'COC': 1, 'LMT': 1, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 4.03, per 1000 atoms: 0.65 Number of scatterers: 6199 At special positions: 0 Unit cell: (75.621, 75.621, 116.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 1104 8.00 N 957 7.00 C 4100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 245 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 58.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.772A pdb=" N PHE A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.532A pdb=" N VAL A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 150 through 153 removed outlier: 3.967A pdb=" N ALA A 153 " --> pdb=" O GLY A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 153' Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.669A pdb=" N HIS A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 193 through 196 removed outlier: 3.581A pdb=" N LYS A 196 " --> pdb=" O PRO A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 197 through 227 removed outlier: 3.929A pdb=" N TYR A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 289 through 307 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.811A pdb=" N VAL A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.626A pdb=" N THR A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.672A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.822A pdb=" N LEU A 358 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 removed outlier: 4.213A pdb=" N TRP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.713A pdb=" N TYR A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 427 removed outlier: 3.659A pdb=" N ASP A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 removed outlier: 4.258A pdb=" N LEU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 490 removed outlier: 3.599A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 4.420A pdb=" N TRP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 4.199A pdb=" N VAL A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'A' and resid 554 through 567 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.844A pdb=" N VAL A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 595 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.696A pdb=" N ILE A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.425A pdb=" N ILE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 648 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.811A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.613A pdb=" N ASP B 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.021A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.549A pdb=" N GLN B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 44 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 35 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 104 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.587A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR B 129 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.587A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.822A pdb=" N SER C 42 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 91 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.857A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.871A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 926 1.31 - 1.44: 1934 1.44 - 1.56: 3453 1.56 - 1.69: 20 1.69 - 1.81: 53 Bond restraints: 6386 Sorted by residual: bond pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " ideal model delta sigma weight residual 1.332 1.556 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAU Y01 A1005 " pdb=" CBI Y01 A1005 " ideal model delta sigma weight residual 1.530 1.719 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" CAU Y01 A1006 " pdb=" CBI Y01 A1006 " ideal model delta sigma weight residual 1.530 1.717 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" CAP Y01 A1006 " pdb=" CBE Y01 A1006 " ideal model delta sigma weight residual 1.553 1.385 0.168 2.00e-02 2.50e+03 7.06e+01 ... (remaining 6381 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.28: 239 107.28 - 113.97: 3562 113.97 - 120.66: 2623 120.66 - 127.35: 2193 127.35 - 134.03: 88 Bond angle restraints: 8705 Sorted by residual: angle pdb=" CAK Y01 A1005 " pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " ideal model delta sigma weight residual 124.96 112.71 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CAK Y01 A1006 " pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 124.96 113.38 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " pdb=" CBH Y01 A1005 " ideal model delta sigma weight residual 123.00 112.65 10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " pdb=" CBH Y01 A1006 " ideal model delta sigma weight residual 123.00 113.08 9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C2 LMT A1007 " pdb=" C3 LMT A1007 " pdb=" C4 LMT A1007 " ideal model delta sigma weight residual 117.09 107.28 9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 8700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3226 17.36 - 34.73: 428 34.73 - 52.09: 135 52.09 - 69.45: 25 69.45 - 86.82: 6 Dihedral angle restraints: 3820 sinusoidal: 1622 harmonic: 2198 Sorted by residual: dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 112 " pdb=" CB CYS C 112 " ideal model delta sinusoidal sigma weight residual 93.00 132.06 -39.06 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 130.23 -37.23 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA GLU C 129 " pdb=" C GLU C 129 " pdb=" N ILE C 130 " pdb=" CA ILE C 130 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 3817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 936 0.097 - 0.193: 29 0.193 - 0.290: 5 0.290 - 0.387: 0 0.387 - 0.483: 2 Chirality restraints: 972 Sorted by residual: chirality pdb=" CBG Y01 A1006 " pdb=" CAQ Y01 A1006 " pdb=" CBD Y01 A1006 " pdb=" CBI Y01 A1006 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CBG Y01 A1005 " pdb=" CAQ Y01 A1005 " pdb=" CBD Y01 A1005 " pdb=" CBI Y01 A1005 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CBI Y01 A1006 " pdb=" CAU Y01 A1006 " pdb=" CBE Y01 A1006 " pdb=" CBG Y01 A1006 " both_signs ideal model delta sigma weight residual False 2.94 2.70 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 969 not shown) Planarity restraints: 1054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 351 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO A 352 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 348 " 0.007 2.00e-02 2.50e+03 9.13e-03 1.46e+00 pdb=" CG PHE A 348 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 348 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 348 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 477 " -0.007 2.00e-02 2.50e+03 8.73e-03 1.33e+00 pdb=" CG PHE A 477 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 477 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 477 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 477 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 477 " 0.000 2.00e-02 2.50e+03 ... (remaining 1051 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 245 2.72 - 3.27: 6105 3.27 - 3.81: 10601 3.81 - 4.36: 12394 4.36 - 4.90: 21440 Nonbonded interactions: 50785 Sorted by model distance: nonbonded pdb=" OD1 ASP A 135 " pdb=" OH TYR A 213 " model vdw 2.178 2.440 nonbonded pdb=" O SER A 596 " pdb=" O6' LMT A1007 " model vdw 2.178 2.440 nonbonded pdb=" O ASN A 182 " pdb=" OG SER A 386 " model vdw 2.227 2.440 nonbonded pdb=" O CYS A 184 " pdb=" NE1 TRP A 188 " model vdw 2.290 2.520 nonbonded pdb=" OG1 THR A 215 " pdb=" OG1 THR A 517 " model vdw 2.295 2.440 ... (remaining 50780 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: 6.890 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: 13.470 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.008 0.225 6386 Z= 0.550 Angle : 0.687 12.253 8705 Z= 0.283 Chirality : 0.047 0.483 972 Planarity : 0.003 0.069 1053 Dihedral : 17.064 86.818 2415 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.16 % Allowed : 29.97 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.32), residues: 759 helix: 1.95 (0.27), residues: 371 sheet: 0.40 (0.61), residues: 87 loop : -1.01 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.001 0.000 HIS A 493 PHE 0.021 0.001 PHE A 348 TYR 0.008 0.001 TYR A 212 ARG 0.001 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.654 Fit side-chains REVERT: A 297 MET cc_start: 0.7686 (tmm) cc_final: 0.5479 (mtt) REVERT: C 78 GLN cc_start: 0.7121 (mt0) cc_final: 0.6910 (mt0) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1584 time to fit residues: 16.4632 Evaluate side-chains 69 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6386 Z= 0.313 Angle : 0.638 9.936 8705 Z= 0.319 Chirality : 0.045 0.316 972 Planarity : 0.005 0.062 1053 Dihedral : 8.398 59.775 1106 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.11 % Allowed : 28.73 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.32), residues: 759 helix: 1.19 (0.26), residues: 373 sheet: 0.48 (0.55), residues: 111 loop : -1.12 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.002 0.001 HIS C 100 PHE 0.036 0.002 PHE A 477 TYR 0.023 0.002 TYR A 212 ARG 0.004 0.001 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.668 Fit side-chains REVERT: A 217 MET cc_start: 0.8195 (mmm) cc_final: 0.7984 (mmm) REVERT: A 297 MET cc_start: 0.7891 (tmm) cc_final: 0.5599 (mtt) REVERT: A 471 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 605 TYR cc_start: 0.6773 (t80) cc_final: 0.5972 (t80) outliers start: 20 outliers final: 11 residues processed: 86 average time/residue: 0.1821 time to fit residues: 21.7641 Evaluate side-chains 79 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6386 Z= 0.237 Angle : 0.528 5.921 8705 Z= 0.268 Chirality : 0.041 0.374 972 Planarity : 0.004 0.050 1053 Dihedral : 7.950 59.741 1105 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.04 % Allowed : 28.42 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.32), residues: 759 helix: 1.25 (0.26), residues: 372 sheet: 0.39 (0.54), residues: 116 loop : -1.00 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.016 0.002 PHE A 477 TYR 0.014 0.001 TYR A 212 ARG 0.002 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 0.632 Fit side-chains REVERT: A 297 MET cc_start: 0.7919 (tmm) cc_final: 0.5579 (mtt) REVERT: A 420 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6756 (mp) REVERT: A 471 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8028 (mp) outliers start: 26 outliers final: 18 residues processed: 90 average time/residue: 0.1340 time to fit residues: 17.7095 Evaluate side-chains 89 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.0070 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6386 Z= 0.137 Angle : 0.467 6.038 8705 Z= 0.239 Chirality : 0.038 0.305 972 Planarity : 0.003 0.042 1053 Dihedral : 7.679 59.996 1105 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.73 % Allowed : 29.81 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.32), residues: 759 helix: 1.55 (0.26), residues: 372 sheet: 0.58 (0.54), residues: 111 loop : -0.95 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 PHE 0.013 0.001 PHE A 603 TYR 0.009 0.001 TYR A 629 ARG 0.001 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 0.652 Fit side-chains REVERT: A 297 MET cc_start: 0.7876 (tmm) cc_final: 0.5505 (mtt) REVERT: A 471 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8051 (mp) outliers start: 24 outliers final: 16 residues processed: 85 average time/residue: 0.1376 time to fit residues: 17.3568 Evaluate side-chains 78 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6386 Z= 0.220 Angle : 0.520 6.540 8705 Z= 0.266 Chirality : 0.041 0.401 972 Planarity : 0.004 0.038 1053 Dihedral : 7.547 59.890 1105 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.75 % Allowed : 27.64 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.32), residues: 759 helix: 1.34 (0.26), residues: 372 sheet: 0.52 (0.54), residues: 114 loop : -0.96 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 PHE 0.023 0.001 PHE A 477 TYR 0.015 0.002 TYR A 212 ARG 0.002 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 0.684 Fit side-chains REVERT: A 297 MET cc_start: 0.7896 (tmm) cc_final: 0.5531 (mtt) REVERT: A 420 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6750 (mp) REVERT: A 447 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 471 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8194 (mp) outliers start: 37 outliers final: 27 residues processed: 96 average time/residue: 0.1276 time to fit residues: 18.3356 Evaluate side-chains 94 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6386 Z= 0.168 Angle : 0.486 5.843 8705 Z= 0.248 Chirality : 0.040 0.355 972 Planarity : 0.003 0.035 1053 Dihedral : 7.268 59.542 1105 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.43 % Allowed : 27.48 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.32), residues: 759 helix: 1.43 (0.26), residues: 371 sheet: 0.53 (0.54), residues: 114 loop : -0.91 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.014 0.001 PHE A 603 TYR 0.010 0.001 TYR A 212 ARG 0.001 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 64 time to evaluate : 0.770 Fit side-chains REVERT: A 297 MET cc_start: 0.7861 (tmm) cc_final: 0.5522 (mtt) REVERT: A 420 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6742 (mp) REVERT: A 447 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: A 471 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8183 (mp) outliers start: 35 outliers final: 26 residues processed: 95 average time/residue: 0.1344 time to fit residues: 19.1140 Evaluate side-chains 92 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 63 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6386 Z= 0.251 Angle : 0.546 7.364 8705 Z= 0.277 Chirality : 0.042 0.344 972 Planarity : 0.004 0.032 1053 Dihedral : 7.242 59.163 1105 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.68 % Allowed : 26.55 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.32), residues: 759 helix: 1.21 (0.26), residues: 371 sheet: 0.53 (0.55), residues: 114 loop : -1.01 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.025 0.002 PHE A 477 TYR 0.015 0.002 TYR A 212 ARG 0.002 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 65 time to evaluate : 0.670 Fit side-chains REVERT: A 228 PHE cc_start: 0.7574 (m-80) cc_final: 0.7314 (m-80) REVERT: A 297 MET cc_start: 0.7893 (tmm) cc_final: 0.5544 (mtt) REVERT: A 420 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6834 (mp) REVERT: A 447 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 471 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 43 outliers final: 34 residues processed: 103 average time/residue: 0.1216 time to fit residues: 18.7687 Evaluate side-chains 102 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6386 Z= 0.222 Angle : 0.531 7.075 8705 Z= 0.270 Chirality : 0.041 0.378 972 Planarity : 0.003 0.031 1053 Dihedral : 7.181 57.887 1105 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.52 % Allowed : 26.86 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.32), residues: 759 helix: 1.22 (0.26), residues: 371 sheet: 0.51 (0.54), residues: 114 loop : -1.01 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.027 0.001 PHE A 348 TYR 0.014 0.001 TYR A 212 ARG 0.002 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 67 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 228 PHE cc_start: 0.7614 (m-80) cc_final: 0.7354 (m-80) REVERT: A 297 MET cc_start: 0.7863 (tmm) cc_final: 0.5543 (mtt) REVERT: A 420 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6785 (mp) REVERT: A 447 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: A 471 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 23 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7968 (mp) outliers start: 42 outliers final: 35 residues processed: 104 average time/residue: 0.1272 time to fit residues: 19.8986 Evaluate side-chains 105 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 66 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.0570 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6386 Z= 0.142 Angle : 0.484 6.469 8705 Z= 0.247 Chirality : 0.039 0.322 972 Planarity : 0.003 0.031 1053 Dihedral : 6.955 55.531 1105 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.81 % Allowed : 28.57 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.32), residues: 759 helix: 1.46 (0.26), residues: 371 sheet: 0.58 (0.54), residues: 114 loop : -0.92 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.020 0.001 PHE A 348 TYR 0.009 0.001 TYR A 629 ARG 0.001 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 0.635 Fit side-chains REVERT: A 228 PHE cc_start: 0.7587 (m-80) cc_final: 0.7290 (m-80) REVERT: A 297 MET cc_start: 0.7857 (tmm) cc_final: 0.5595 (mtt) REVERT: A 420 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6812 (mp) REVERT: A 447 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: A 471 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 477 PHE cc_start: 0.7821 (m-10) cc_final: 0.7398 (m-80) outliers start: 31 outliers final: 25 residues processed: 92 average time/residue: 0.1396 time to fit residues: 18.8882 Evaluate side-chains 93 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6386 Z= 0.168 Angle : 0.504 8.997 8705 Z= 0.255 Chirality : 0.039 0.335 972 Planarity : 0.003 0.030 1053 Dihedral : 6.856 54.533 1105 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.66 % Allowed : 28.73 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.32), residues: 759 helix: 1.43 (0.26), residues: 371 sheet: 0.74 (0.55), residues: 108 loop : -0.94 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.017 0.001 PHE A 603 TYR 0.010 0.001 TYR A 212 ARG 0.001 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 0.658 Fit side-chains REVERT: A 228 PHE cc_start: 0.7597 (m-80) cc_final: 0.7316 (m-80) REVERT: A 297 MET cc_start: 0.7859 (tmm) cc_final: 0.5585 (mtt) REVERT: A 420 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6821 (mp) REVERT: A 447 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: A 471 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 595 MET cc_start: 0.6636 (ttm) cc_final: 0.6259 (ttp) outliers start: 30 outliers final: 26 residues processed: 91 average time/residue: 0.1347 time to fit residues: 17.9753 Evaluate side-chains 94 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.186037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162399 restraints weight = 6536.218| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.47 r_work: 0.3790 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6386 Z= 0.147 Angle : 0.484 6.140 8705 Z= 0.247 Chirality : 0.039 0.321 972 Planarity : 0.003 0.031 1053 Dihedral : 6.644 53.639 1105 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.12 % Allowed : 28.42 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.32), residues: 759 helix: 1.53 (0.26), residues: 371 sheet: 0.78 (0.55), residues: 108 loop : -0.91 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.022 0.001 PHE A 477 TYR 0.009 0.001 TYR A 629 ARG 0.001 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.22 seconds wall clock time: 33 minutes 2.08 seconds (1982.08 seconds total)