Starting phenix.real_space_refine on Mon Oct 14 14:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/10_2024/8ptj_17872.cif" } resolution = 2.86 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 18 5.49 5 S 54 5.16 5 C 5616 2.51 5 N 1587 2.21 5 O 1757 1.98 5 H 8841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 17874 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7862 Classifications: {'peptide': 511} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain breaks: 1 Chain: "C" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2792 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Chain: "D" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 192 Classifications: {'RNA': 6} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Conformer: "B" Number of residues, atoms: 6, 192 Classifications: {'RNA': 6} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 3} bond proxies already assigned to first conformer: 106 Chain: "V" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 45.530 46.138 18.978 1.00 67.01 S ATOM 4472 SG CYS A 282 43.431 44.368 16.160 1.00 66.74 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A A D 12 " occ=0.60 ... (64 atoms not shown) pdb=" H2 B A D 12 " occ=0.40 residue: pdb=" P A U D 13 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 13 " occ=0.40 residue: pdb=" P A U D 14 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 14 " occ=0.40 Time building chain proxies: 8.20, per 1000 atoms: 0.46 Number of scatterers: 17874 At special positions: 0 Unit cell: (88.2, 87.36, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 18 15.00 O 1757 8.00 N 1587 7.00 C 5616 6.00 H 8841 1.00 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 - 3.00 Amino acid : True - 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: 6.69 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 2 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 45.0% alpha, 12.3% beta 2 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.931A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.719A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.395A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.866A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.669A pdb=" N TYR A 386 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.617A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.713A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.769A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.651A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.824A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.562A pdb=" N SER B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.589A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.999A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 455 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.387A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.592A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.592A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.083A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 385 through 388 removed outlier: 6.501A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 8811 1.05 - 1.25: 1477 1.25 - 1.46: 3622 1.46 - 1.67: 4094 1.67 - 1.88: 77 Bond restraints: 18081 Sorted by residual: bond pdb=" O3'B U D 14 " pdb=" P U D 15 " ideal model delta sigma weight residual 1.607 1.879 -0.272 1.50e-02 4.44e+03 3.28e+02 bond pdb=" N GLN C 88 " pdb=" CA GLN C 88 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.74e+00 bond pdb=" N ILE C 92 " pdb=" CA ILE C 92 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N THR C 87 " pdb=" H THR C 87 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.32e+00 ... (remaining 18076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 32182 1.54 - 3.08: 409 3.08 - 4.62: 53 4.62 - 6.17: 6 6.17 - 7.71: 1 Bond angle restraints: 32651 Sorted by residual: angle pdb=" O3'B U D 14 " pdb=" P U D 15 " pdb=" O5' U D 15 " ideal model delta sigma weight residual 104.00 96.29 7.71 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C3'B U D 14 " pdb=" O3'B U D 14 " pdb=" P U D 15 " ideal model delta sigma weight residual 120.20 126.06 -5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" O THR C 87 " ideal model delta sigma weight residual 121.81 117.61 4.20 1.18e+00 7.18e-01 1.27e+01 angle pdb=" C GLU C 90 " pdb=" N ALA C 91 " pdb=" CA ALA C 91 " ideal model delta sigma weight residual 120.54 125.25 -4.71 1.35e+00 5.49e-01 1.22e+01 angle pdb=" C GLN C 88 " pdb=" N GLU C 89 " pdb=" CA GLU C 89 " ideal model delta sigma weight residual 120.54 125.19 -4.65 1.35e+00 5.49e-01 1.18e+01 ... (remaining 32646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7491 17.80 - 35.60: 678 35.60 - 53.39: 267 53.39 - 71.19: 72 71.19 - 88.99: 20 Dihedral angle restraints: 8528 sinusoidal: 4821 harmonic: 3707 Sorted by residual: dihedral pdb=" CA SER A 19 " pdb=" C SER A 19 " pdb=" N GLU A 20 " pdb=" CA GLU A 20 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP B 213 " pdb=" CB ASP B 213 " pdb=" CG ASP B 213 " pdb=" OD1 ASP B 213 " ideal model delta sinusoidal sigma weight residual -30.00 -86.21 56.21 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE1 GLU B 29 " ideal model delta sinusoidal sigma weight residual 0.00 88.51 -88.51 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1008 0.032 - 0.063: 298 0.063 - 0.095: 68 0.095 - 0.126: 50 0.126 - 0.158: 3 Chirality restraints: 1427 Sorted by residual: chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA LEU C 86 " pdb=" N LEU C 86 " pdb=" C LEU C 86 " pdb=" CB LEU C 86 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1424 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " -0.203 9.50e-02 1.11e+02 6.80e-02 5.70e+00 pdb=" NE ARG A 34 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 34 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 34 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 34 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 34 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 217 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 218 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.019 2.00e-02 2.50e+03 7.50e-03 1.83e+00 pdb=" N9 A V 4 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.001 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 538 2.14 - 2.76: 33099 2.76 - 3.37: 50583 3.37 - 3.99: 66482 3.99 - 4.60: 103404 Nonbonded interactions: 254106 Sorted by model distance: nonbonded pdb="HG21 THR A 236 " pdb=" OP1B U D 13 " model vdw 1.529 2.620 nonbonded pdb=" OE1 GLU B 119 " pdb=" H GLU B 119 " model vdw 1.532 2.450 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU B 381 " pdb=" H PHE B 420 " model vdw 1.620 2.450 nonbonded pdb=" O PHE A 55 " pdb="HH11 ARG A 62 " model vdw 1.642 2.450 ... (remaining 254101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.40 max=1.00 mean=0.99 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: 14.560 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 55.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 9240 Z= 0.221 Angle : 0.485 7.708 12559 Z= 0.273 Chirality : 0.036 0.158 1427 Planarity : 0.004 0.089 1550 Dihedral : 17.879 88.990 3586 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 20.38 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1090 helix: 2.18 (0.26), residues: 446 sheet: -0.21 (0.53), residues: 99 loop : -0.16 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.018 0.001 PHE B 407 TYR 0.008 0.001 TYR A 403 ARG 0.014 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.8886 (tt0) cc_final: 0.8686 (tt0) REVERT: C 89 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 93 ASP cc_start: 0.8323 (m-30) cc_final: 0.7928 (m-30) REVERT: C 113 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (t) outliers start: 27 outliers final: 23 residues processed: 124 average time/residue: 2.6283 time to fit residues: 349.6878 Evaluate side-chains 118 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9240 Z= 0.223 Angle : 0.479 4.830 12559 Z= 0.250 Chirality : 0.037 0.134 1427 Planarity : 0.004 0.040 1550 Dihedral : 10.621 73.556 1508 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.82 % Allowed : 19.54 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1090 helix: 2.14 (0.25), residues: 451 sheet: -0.30 (0.52), residues: 107 loop : -0.22 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.020 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.641 Fit side-chains REVERT: A 34 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7266 (ttp-110) REVERT: A 323 ASP cc_start: 0.8502 (t0) cc_final: 0.8193 (t0) REVERT: A 326 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: B 497 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8332 (tp) REVERT: C 90 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 93 ASP cc_start: 0.8381 (m-30) cc_final: 0.8149 (m-30) REVERT: C 113 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8071 (t) outliers start: 27 outliers final: 12 residues processed: 120 average time/residue: 2.9027 time to fit residues: 373.8326 Evaluate side-chains 112 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9240 Z= 0.251 Angle : 0.480 4.248 12559 Z= 0.250 Chirality : 0.037 0.129 1427 Planarity : 0.004 0.037 1550 Dihedral : 10.326 73.583 1487 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.93 % Allowed : 19.44 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1090 helix: 2.14 (0.25), residues: 450 sheet: -0.37 (0.51), residues: 107 loop : -0.29 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.021 0.001 PHE B 407 TYR 0.011 0.001 TYR A 403 ARG 0.002 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7615 (mtm180) REVERT: A 118 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: A 323 ASP cc_start: 0.8584 (t0) cc_final: 0.8221 (t0) REVERT: A 326 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: C 93 ASP cc_start: 0.8423 (m-30) cc_final: 0.8220 (m-30) REVERT: C 113 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8020 (t) outliers start: 28 outliers final: 15 residues processed: 125 average time/residue: 2.8490 time to fit residues: 381.3118 Evaluate side-chains 116 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9240 Z= 0.211 Angle : 0.465 4.061 12559 Z= 0.243 Chirality : 0.037 0.129 1427 Planarity : 0.004 0.037 1550 Dihedral : 10.083 73.564 1484 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.51 % Allowed : 19.54 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1090 helix: 2.18 (0.25), residues: 451 sheet: -0.33 (0.47), residues: 125 loop : -0.30 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.020 0.001 PHE B 407 TYR 0.011 0.001 TYR A 403 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7591 (mtm180) REVERT: A 323 ASP cc_start: 0.8532 (t0) cc_final: 0.8200 (t0) REVERT: A 326 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: C 93 ASP cc_start: 0.8450 (m-30) cc_final: 0.8241 (m-30) REVERT: C 113 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8022 (t) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 2.8948 time to fit residues: 361.1499 Evaluate side-chains 114 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9240 Z= 0.229 Angle : 0.464 4.015 12559 Z= 0.243 Chirality : 0.037 0.128 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.031 73.586 1482 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.82 % Allowed : 19.44 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1090 helix: 2.18 (0.25), residues: 450 sheet: -0.38 (0.46), residues: 125 loop : -0.32 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.020 0.001 PHE B 407 TYR 0.011 0.001 TYR A 403 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8527 (t0) cc_final: 0.8180 (t0) REVERT: A 326 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: C 93 ASP cc_start: 0.8454 (m-30) cc_final: 0.8239 (m-30) REVERT: C 113 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8031 (t) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 2.8582 time to fit residues: 366.1799 Evaluate side-chains 121 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9240 Z= 0.324 Angle : 0.504 5.023 12559 Z= 0.264 Chirality : 0.038 0.129 1427 Planarity : 0.004 0.040 1550 Dihedral : 10.086 73.602 1481 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 3.45 % Allowed : 19.44 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1090 helix: 2.05 (0.25), residues: 450 sheet: -0.44 (0.46), residues: 125 loop : -0.39 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.022 0.001 PHE B 407 TYR 0.011 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7568 (mtm180) REVERT: A 323 ASP cc_start: 0.8586 (t0) cc_final: 0.8192 (t0) REVERT: A 326 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: C 93 ASP cc_start: 0.8445 (m-30) cc_final: 0.8232 (m-30) REVERT: C 113 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8075 (t) outliers start: 33 outliers final: 20 residues processed: 122 average time/residue: 2.9823 time to fit residues: 387.8721 Evaluate side-chains 119 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9240 Z= 0.226 Angle : 0.473 4.175 12559 Z= 0.247 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.053 73.591 1481 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.24 % Allowed : 19.64 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1090 helix: 2.13 (0.25), residues: 450 sheet: -0.45 (0.46), residues: 125 loop : -0.35 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.021 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8511 (t0) cc_final: 0.8127 (t0) REVERT: A 326 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 391 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: C 93 ASP cc_start: 0.8442 (m-30) cc_final: 0.8208 (m-30) REVERT: C 113 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (t) outliers start: 31 outliers final: 21 residues processed: 123 average time/residue: 2.8234 time to fit residues: 371.5856 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9240 Z= 0.227 Angle : 0.473 4.479 12559 Z= 0.247 Chirality : 0.037 0.129 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.048 73.597 1481 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.03 % Allowed : 19.96 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1090 helix: 2.16 (0.25), residues: 450 sheet: -0.47 (0.46), residues: 125 loop : -0.35 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.021 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8522 (t0) cc_final: 0.8161 (t0) REVERT: A 326 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: C 93 ASP cc_start: 0.8445 (m-30) cc_final: 0.8233 (m-30) REVERT: C 113 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8050 (t) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 2.9628 time to fit residues: 381.7772 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9240 Z= 0.266 Angle : 0.489 6.225 12559 Z= 0.255 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.092 73.605 1481 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.03 % Allowed : 20.06 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1090 helix: 2.11 (0.25), residues: 450 sheet: -0.50 (0.46), residues: 125 loop : -0.35 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.021 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8541 (t0) cc_final: 0.8166 (t0) REVERT: A 326 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 93 ASP cc_start: 0.8445 (m-30) cc_final: 0.8225 (m-30) REVERT: C 113 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8059 (t) outliers start: 29 outliers final: 22 residues processed: 118 average time/residue: 2.8961 time to fit residues: 368.2495 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9240 Z= 0.209 Angle : 0.469 5.870 12559 Z= 0.244 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.063 73.586 1481 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.82 % Allowed : 20.27 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1090 helix: 2.19 (0.25), residues: 450 sheet: -0.46 (0.46), residues: 125 loop : -0.32 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.020 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.005 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8529 (t0) cc_final: 0.8178 (t0) REVERT: A 326 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: C 113 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8062 (t) outliers start: 27 outliers final: 21 residues processed: 118 average time/residue: 2.7341 time to fit residues: 345.8974 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.075391 restraints weight = 50133.186| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.16 r_work: 0.2646 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9240 Z= 0.175 Angle : 0.457 5.892 12559 Z= 0.237 Chirality : 0.036 0.129 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.004 73.580 1481 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 20.17 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1090 helix: 2.27 (0.25), residues: 451 sheet: -0.44 (0.46), residues: 125 loop : -0.31 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.019 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.005 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7014.06 seconds wall clock time: 127 minutes 27.49 seconds (7647.49 seconds total)