Starting phenix.real_space_refine on Mon Mar 11 09:31:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp7_25367/03_2024/7sp7_25367.pdb" } resolution = 3.1 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1820 atoms to isotropic. 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 Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3914 2.51 5 N 991 2.21 5 O 1107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 bond proxies already assigned to first conformer: 4152 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MN': 2, '3PE': 1, 'UDP': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 303 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 303 " occ=0.50 Time building chain proxies: 5.70, per 1000 atoms: 0.94 Number of scatterers: 6052 At special positions: 0 Unit cell: (71.28, 73.44, 154.44, 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) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1107 8.00 N 991 7.00 C 3914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 46.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.683A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.968A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.044A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.510A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.502A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.634A pdb=" N TRP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 5.337A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.982A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 removed outlier: 4.542A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.811A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 3.778A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 470 through 497 removed outlier: 6.382A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.538A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.554A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.773A pdb=" N ILE A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 273 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 229 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.459A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.621A pdb=" N VAL B 12 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.814A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 97 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 113 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.814A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.795A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 82 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.795A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.877A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 931 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: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 935 1.28 - 1.41: 1717 1.41 - 1.55: 3459 1.55 - 1.68: 38 1.68 - 1.81: 54 Bond restraints: 6203 Sorted by residual: bond pdb=" C3' UDP A 603 " pdb=" C2' UDP A 603 " ideal model delta sigma weight residual 1.530 1.300 0.230 1.30e-02 5.92e+03 3.14e+02 bond pdb=" C5 UDP A 603 " pdb=" C6 UDP A 603 " ideal model delta sigma weight residual 1.343 1.511 -0.168 1.60e-02 3.91e+03 1.11e+02 bond pdb=" C5' UDP A 603 " pdb=" C4' UDP A 603 " ideal model delta sigma weight residual 1.508 1.397 0.111 1.10e-02 8.26e+03 1.01e+02 bond pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " ideal model delta sigma weight residual 1.375 1.517 -0.142 1.70e-02 3.46e+03 7.00e+01 bond pdb=" O3A UDP A 603 " pdb=" PB UDP A 603 " ideal model delta sigma weight residual 1.584 1.659 -0.075 1.00e-02 1.00e+04 5.67e+01 ... (remaining 6198 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.93: 97 105.93 - 112.95: 3264 112.95 - 119.96: 2133 119.96 - 126.97: 2849 126.97 - 133.98: 72 Bond angle restraints: 8415 Sorted by residual: angle pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " pdb=" C4 UDP A 603 " ideal model delta sigma weight residual 126.93 120.20 6.73 1.00e+00 1.00e+00 4.54e+01 angle pdb=" O2B UDP A 603 " pdb=" PB UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 102.95 109.61 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" O1B UDP A 603 " pdb=" PB UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 102.95 109.42 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" O5' UDP A 603 " pdb=" PA UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 104.35 109.91 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" N1 UDP A 603 " pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " ideal model delta sigma weight residual 114.79 120.18 -5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 8410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 3602 34.01 - 68.02: 72 68.02 - 102.03: 11 102.03 - 136.04: 0 136.04 - 170.05: 1 Dihedral angle restraints: 3686 sinusoidal: 1529 harmonic: 2157 Sorted by residual: dihedral pdb=" O21 3PE A 601 " pdb=" C2 3PE A 601 " pdb=" C3 3PE A 601 " pdb=" O31 3PE A 601 " ideal model delta sinusoidal sigma weight residual 60.47 -129.48 -170.05 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 54.45 38.55 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB LYS A 314 " pdb=" CG LYS A 314 " pdb=" CD LYS A 314 " pdb=" CE LYS A 314 " ideal model delta sinusoidal sigma weight residual 60.00 116.86 -56.86 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 3683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 841 0.080 - 0.161: 62 0.161 - 0.241: 3 0.241 - 0.322: 2 0.322 - 0.402: 3 Chirality restraints: 911 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBE Y01 A 602 " pdb=" CAP Y01 A 602 " pdb=" CBB Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.57 2.92 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CBI Y01 A 602 " pdb=" CAU Y01 A 602 " pdb=" CBE Y01 A 602 " pdb=" CBG Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 908 not shown) Planarity restraints: 1034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.52e-01 pdb=" N PRO A 320 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 251 " -0.005 2.00e-02 2.50e+03 9.08e-03 8.24e-01 pdb=" C ALA A 251 " 0.016 2.00e-02 2.50e+03 pdb=" O ALA A 251 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE A 252 " -0.005 2.00e-02 2.50e+03 ... (remaining 1031 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 653 2.75 - 3.29: 5636 3.29 - 3.83: 10081 3.83 - 4.36: 11184 4.36 - 4.90: 20097 Nonbonded interactions: 47651 Sorted by model distance: nonbonded pdb=" OD2 ASP B 72 " pdb=" OG1 THR B 74 " model vdw 2.219 2.440 nonbonded pdb=" O3' UDP A 603 " pdb=" O2' UDP A 603 " model vdw 2.367 2.432 nonbonded pdb=" OE1 GLN A 186 " pdb=" NZ LYS A 284 " model vdw 2.391 2.520 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.397 2.440 nonbonded pdb=" OG SER C 17 " pdb=" O MET C 82 " model vdw 2.401 2.440 ... (remaining 47646 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.770 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 0.230 6203 Z= 0.495 Angle : 0.681 14.565 8415 Z= 0.331 Chirality : 0.047 0.402 911 Planarity : 0.002 0.035 1034 Dihedral : 14.829 170.050 2308 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.32), residues: 732 helix: 2.79 (0.29), residues: 317 sheet: 1.89 (0.44), residues: 142 loop : 0.20 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 502 HIS 0.001 0.000 HIS A 360 PHE 0.007 0.001 PHE A 249 TYR 0.009 0.001 TYR A 430 ARG 0.002 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.777 Fit side-chains REVERT: A 372 MET cc_start: 0.7350 (mmt) cc_final: 0.7042 (mmt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1748 time to fit residues: 25.2057 Evaluate side-chains 81 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6203 Z= 0.177 Angle : 0.459 7.722 8415 Z= 0.242 Chirality : 0.041 0.217 911 Planarity : 0.003 0.034 1034 Dihedral : 9.794 140.931 980 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.32), residues: 732 helix: 2.81 (0.30), residues: 319 sheet: 1.90 (0.42), residues: 155 loop : 0.11 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 358 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE B 47 TYR 0.019 0.001 TYR A 492 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.653 Fit side-chains REVERT: A 372 MET cc_start: 0.7494 (mmt) cc_final: 0.7092 (mmt) REVERT: B 52 SER cc_start: 0.8478 (m) cc_final: 0.8137 (t) REVERT: B 72 ASP cc_start: 0.6454 (t70) cc_final: 0.6033 (t70) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 0.2043 time to fit residues: 23.7707 Evaluate side-chains 82 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6203 Z= 0.236 Angle : 0.498 4.994 8415 Z= 0.270 Chirality : 0.043 0.239 911 Planarity : 0.004 0.036 1034 Dihedral : 9.647 120.827 980 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.43 % Allowed : 8.40 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.31), residues: 732 helix: 2.44 (0.29), residues: 326 sheet: 1.61 (0.41), residues: 155 loop : -0.24 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.017 0.002 PHE B 47 TYR 0.018 0.001 TYR A 492 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.671 Fit side-chains REVERT: A 84 VAL cc_start: 0.8832 (p) cc_final: 0.8623 (m) REVERT: A 372 MET cc_start: 0.7615 (mmt) cc_final: 0.7215 (mmt) REVERT: B 52 SER cc_start: 0.8794 (m) cc_final: 0.8401 (t) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1531 time to fit residues: 16.5275 Evaluate side-chains 74 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6203 Z= 0.177 Angle : 0.437 4.945 8415 Z= 0.237 Chirality : 0.041 0.236 911 Planarity : 0.003 0.037 1034 Dihedral : 9.470 114.489 980 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.43 % Allowed : 10.30 % Favored : 88.27 % 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: 1.97 (0.31), residues: 732 helix: 2.47 (0.29), residues: 326 sheet: 1.39 (0.40), residues: 159 loop : -0.36 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.012 0.001 PHE B 47 TYR 0.016 0.001 TYR A 492 ARG 0.004 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.668 Fit side-chains REVERT: A 372 MET cc_start: 0.7334 (mmt) cc_final: 0.6930 (mmt) REVERT: B 52 SER cc_start: 0.8715 (m) cc_final: 0.8375 (t) REVERT: B 79 SER cc_start: 0.7891 (p) cc_final: 0.7678 (m) outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.1486 time to fit residues: 17.0181 Evaluate side-chains 78 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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: 0.7428 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6203 Z= 0.238 Angle : 0.482 5.039 8415 Z= 0.261 Chirality : 0.042 0.223 911 Planarity : 0.003 0.035 1034 Dihedral : 9.321 103.073 980 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.22 % Allowed : 11.57 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 732 helix: 2.32 (0.29), residues: 326 sheet: 1.10 (0.40), residues: 161 loop : -0.45 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.015 0.001 PHE B 47 TYR 0.016 0.001 TYR A 492 ARG 0.005 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.607 Fit side-chains REVERT: A 372 MET cc_start: 0.7462 (mmt) cc_final: 0.7046 (mmt) REVERT: B 52 SER cc_start: 0.8835 (m) cc_final: 0.8471 (t) REVERT: B 64 LYS cc_start: 0.6640 (mmmt) cc_final: 0.6335 (mmtt) outliers start: 14 outliers final: 13 residues processed: 79 average time/residue: 0.1578 time to fit residues: 17.4314 Evaluate side-chains 77 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7419 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6203 Z= 0.196 Angle : 0.449 5.088 8415 Z= 0.244 Chirality : 0.041 0.217 911 Planarity : 0.003 0.035 1034 Dihedral : 8.890 85.114 980 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.38 % Allowed : 11.25 % Favored : 86.37 % 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: 1.68 (0.31), residues: 732 helix: 2.29 (0.29), residues: 326 sheet: 1.28 (0.41), residues: 148 loop : -0.53 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.011 0.001 PHE B 47 TYR 0.015 0.001 TYR A 492 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.684 Fit side-chains REVERT: B 52 SER cc_start: 0.8794 (m) cc_final: 0.8479 (t) REVERT: B 64 LYS cc_start: 0.6930 (mmmt) cc_final: 0.6590 (mmtt) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1591 time to fit residues: 17.2871 Evaluate side-chains 75 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7438 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6203 Z= 0.218 Angle : 0.471 5.041 8415 Z= 0.253 Chirality : 0.042 0.197 911 Planarity : 0.003 0.037 1034 Dihedral : 7.813 85.020 980 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.69 % Allowed : 11.73 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 732 helix: 2.25 (0.29), residues: 326 sheet: 0.98 (0.39), residues: 160 loop : -0.52 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.013 0.001 PHE B 47 TYR 0.016 0.001 TYR A 430 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.681 Fit side-chains REVERT: B 52 SER cc_start: 0.8808 (m) cc_final: 0.8491 (t) REVERT: B 64 LYS cc_start: 0.6769 (mmmt) cc_final: 0.6445 (mmtt) outliers start: 17 outliers final: 16 residues processed: 80 average time/residue: 0.1589 time to fit residues: 17.7583 Evaluate side-chains 79 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7432 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6203 Z= 0.197 Angle : 0.450 5.536 8415 Z= 0.245 Chirality : 0.041 0.185 911 Planarity : 0.003 0.037 1034 Dihedral : 7.693 85.351 980 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.54 % Allowed : 11.57 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 732 helix: 2.30 (0.29), residues: 326 sheet: 1.14 (0.41), residues: 145 loop : -0.61 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.011 0.001 PHE B 47 TYR 0.016 0.001 TYR C 106 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.669 Fit side-chains REVERT: B 52 SER cc_start: 0.8786 (m) cc_final: 0.8451 (t) REVERT: B 64 LYS cc_start: 0.6810 (mmmt) cc_final: 0.6488 (mmtt) outliers start: 16 outliers final: 15 residues processed: 76 average time/residue: 0.1543 time to fit residues: 16.3452 Evaluate side-chains 78 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6203 Z= 0.272 Angle : 0.502 5.798 8415 Z= 0.271 Chirality : 0.043 0.185 911 Planarity : 0.003 0.036 1034 Dihedral : 7.925 82.932 980 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 11.73 % Favored : 85.74 % 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: 1.48 (0.31), residues: 732 helix: 2.14 (0.29), residues: 326 sheet: 0.93 (0.39), residues: 156 loop : -0.54 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.015 0.001 PHE B 47 TYR 0.015 0.001 TYR C 106 ARG 0.003 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.626 Fit side-chains REVERT: B 52 SER cc_start: 0.8850 (m) cc_final: 0.8506 (t) REVERT: B 64 LYS cc_start: 0.6946 (mmmt) cc_final: 0.6565 (mmtt) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.1609 time to fit residues: 17.2517 Evaluate side-chains 75 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6203 Z= 0.180 Angle : 0.453 5.996 8415 Z= 0.247 Chirality : 0.041 0.175 911 Planarity : 0.003 0.037 1034 Dihedral : 7.708 84.493 980 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.38 % Allowed : 11.57 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.31), residues: 732 helix: 2.29 (0.29), residues: 326 sheet: 1.09 (0.41), residues: 145 loop : -0.67 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.001 0.001 HIS A 552 PHE 0.011 0.001 PHE A 49 TYR 0.016 0.001 TYR C 106 ARG 0.006 0.000 ARG A 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.703 Fit side-chains REVERT: B 52 SER cc_start: 0.8766 (m) cc_final: 0.8440 (t) REVERT: B 64 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6478 (mmtt) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1573 time to fit residues: 16.9579 Evaluate side-chains 78 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105347 restraints weight = 16479.330| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.28 r_work: 0.3198 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6203 Z= 0.197 Angle : 0.467 6.036 8415 Z= 0.252 Chirality : 0.041 0.174 911 Planarity : 0.003 0.037 1034 Dihedral : 7.685 85.117 980 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.22 % Allowed : 12.20 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.31), residues: 732 helix: 2.29 (0.29), residues: 326 sheet: 1.11 (0.40), residues: 149 loop : -0.67 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.012 0.001 PHE A 49 TYR 0.016 0.001 TYR C 106 ARG 0.008 0.001 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1611.37 seconds wall clock time: 29 minutes 50.39 seconds (1790.39 seconds total)