Starting phenix.real_space_refine on Sat Dec 28 07:46:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sp7_25367/12_2024/7sp7_25367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp7_25367/12_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/cci-nas-00/data/ceres_data/7sp7_25367/12_2024/7sp7_25367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp7_25367/12_2024/7sp7_25367.map" model { file = "/net/cci-nas-00/data/ceres_data/7sp7_25367/12_2024/7sp7_25367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp7_25367/12_2024/7sp7_25367.cif" } 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. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.09, per 1000 atoms: 1.01 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 - 3.00 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: 1.77 Conformation dependent library (CDL) restraints added in 1.4 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: 0.67 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: 1.84 Time building geometry restraints manager: 1.88 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: 0.00 - 2.91: 8307 2.91 - 5.83: 88 5.83 - 8.74: 14 8.74 - 11.65: 3 11.65 - 14.56: 3 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 3.040 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 3.120 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.397 3.040 nonbonded pdb=" OG SER C 17 " pdb=" O MET C 82 " model vdw 2.401 3.040 ... (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 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=0.50 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: 1.150 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.669 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: 0.1808 time to fit residues: 26.1534 Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 0.0030 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 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: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1714 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 : 0.470 7.865 8415 Z= 0.250 Chirality : 0.042 0.237 911 Planarity : 0.003 0.034 1034 Dihedral : 9.742 140.610 980 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.63 % Allowed : 6.50 % Favored : 92.87 % 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: 2.48 (0.32), residues: 732 helix: 2.76 (0.29), residues: 319 sheet: 1.74 (0.42), residues: 157 loop : 0.14 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 358 HIS 0.001 0.001 HIS A 552 PHE 0.014 0.001 PHE B 47 TYR 0.020 0.001 TYR A 492 ARG 0.003 0.000 ARG A 256 *********************** 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 92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.661 Fit side-chains REVERT: A 372 MET cc_start: 0.7494 (mmt) cc_final: 0.7066 (mmt) REVERT: B 72 ASP cc_start: 0.6789 (t70) cc_final: 0.6560 (t70) REVERT: B 86 LYS cc_start: 0.7134 (ptpp) cc_final: 0.6898 (ptpp) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.1942 time to fit residues: 22.9747 Evaluate side-chains 82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 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: 1.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7363 moved from start: 0.3089 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= 0.207 Angle : 0.490 4.958 8415 Z= 0.266 Chirality : 0.043 0.226 911 Planarity : 0.004 0.037 1034 Dihedral : 9.562 116.112 980 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.58 % Allowed : 7.92 % Favored : 90.49 % 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: 2.06 (0.31), residues: 732 helix: 2.49 (0.29), residues: 325 sheet: 1.42 (0.41), residues: 161 loop : -0.23 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 351 HIS 0.002 0.001 HIS A 174 PHE 0.015 0.001 PHE B 47 TYR 0.019 0.001 TYR A 492 ARG 0.008 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 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.751 Fit side-chains REVERT: A 372 MET cc_start: 0.7592 (mmt) cc_final: 0.7186 (mmt) REVERT: A 391 LYS cc_start: 0.6895 (mptt) cc_final: 0.6511 (mptt) REVERT: C 75 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.8094 (mtm-85) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1730 time to fit residues: 18.7114 Evaluate side-chains 73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP 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 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: 5.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7396 moved from start: 0.3516 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= 0.215 Angle : 0.476 5.339 8415 Z= 0.258 Chirality : 0.042 0.229 911 Planarity : 0.003 0.036 1034 Dihedral : 9.660 115.289 980 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.43 % Allowed : 9.83 % Favored : 88.75 % 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: 1.83 (0.31), residues: 732 helix: 2.39 (0.29), residues: 325 sheet: 1.18 (0.41), residues: 161 loop : -0.37 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.014 0.001 PHE B 47 TYR 0.016 0.001 TYR A 492 ARG 0.007 0.001 ARG C 19 *********************** 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 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.705 Fit side-chains REVERT: A 190 MET cc_start: 0.8141 (mmm) cc_final: 0.7905 (mtp) REVERT: A 372 MET cc_start: 0.7473 (mmt) cc_final: 0.7064 (mmt) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.1758 time to fit residues: 17.7097 Evaluate side-chains 73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 52 SER 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6203 Z= 0.214 Angle : 0.472 5.006 8415 Z= 0.256 Chirality : 0.042 0.189 911 Planarity : 0.003 0.037 1034 Dihedral : 9.511 103.558 980 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.06 % Allowed : 10.78 % Favored : 87.16 % 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: 1.74 (0.31), residues: 732 helix: 2.33 (0.29), residues: 325 sheet: 1.20 (0.41), residues: 150 loop : -0.42 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 351 HIS 0.001 0.001 HIS A 552 PHE 0.013 0.001 PHE B 47 TYR 0.016 0.001 TYR A 492 ARG 0.006 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 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.732 Fit side-chains REVERT: A 372 MET cc_start: 0.7420 (mmt) cc_final: 0.7211 (mmt) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.1724 time to fit residues: 18.1618 Evaluate side-chains 72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 52 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7430 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6203 Z= 0.220 Angle : 0.469 5.106 8415 Z= 0.255 Chirality : 0.042 0.171 911 Planarity : 0.003 0.037 1034 Dihedral : 9.262 86.840 980 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.90 % Allowed : 10.94 % Favored : 87.16 % 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: 1.63 (0.31), residues: 732 helix: 2.26 (0.28), residues: 325 sheet: 1.07 (0.41), residues: 150 loop : -0.46 (0.36), residues: 257 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 0.013 0.001 PHE B 47 TYR 0.015 0.001 TYR A 492 ARG 0.005 0.001 ARG C 19 *********************** 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 75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.661 Fit side-chains REVERT: A 304 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7366 (tpt170) REVERT: A 372 MET cc_start: 0.7479 (mmt) cc_final: 0.7223 (mmt) REVERT: B 64 LYS cc_start: 0.6846 (mmmt) cc_final: 0.6511 (mmtt) outliers start: 12 outliers final: 12 residues processed: 73 average time/residue: 0.1811 time to fit residues: 18.0878 Evaluate side-chains 74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 52 SER 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 46 GLU 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: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.4161 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= 0.203 Angle : 0.464 5.457 8415 Z= 0.251 Chirality : 0.041 0.155 911 Planarity : 0.003 0.038 1034 Dihedral : 7.980 85.812 980 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.38 % Allowed : 11.09 % Favored : 86.53 % 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: 1.64 (0.31), residues: 732 helix: 2.28 (0.29), residues: 325 sheet: 1.06 (0.41), residues: 150 loop : -0.46 (0.37), residues: 257 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 0.011 0.001 PHE B 47 TYR 0.019 0.001 TYR C 106 ARG 0.005 0.001 ARG C 19 *********************** 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 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.598 Fit side-chains REVERT: A 304 ARG cc_start: 0.7623 (tpt170) cc_final: 0.7312 (tpt170) REVERT: A 372 MET cc_start: 0.7555 (mmt) cc_final: 0.7215 (mmt) REVERT: B 64 LYS cc_start: 0.6908 (mmmt) cc_final: 0.6592 (mmtt) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1798 time to fit residues: 19.2021 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 52 SER 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 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ASN 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: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.0020 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 overall best weight: 0.4946 ------------------------------------------------------------------------------- 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: 0.7407 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6203 Z= 0.148 Angle : 0.427 5.738 8415 Z= 0.232 Chirality : 0.040 0.136 911 Planarity : 0.003 0.039 1034 Dihedral : 7.740 87.871 980 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.06 % Allowed : 11.57 % 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: 1.70 (0.31), residues: 732 helix: 2.39 (0.29), residues: 325 sheet: 0.83 (0.40), residues: 160 loop : -0.37 (0.38), residues: 247 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 0.009 0.001 PHE A 385 TYR 0.015 0.001 TYR C 106 ARG 0.004 0.000 ARG C 19 *********************** 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 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.637 Fit side-chains REVERT: A 372 MET cc_start: 0.7375 (mmt) cc_final: 0.7081 (mmt) REVERT: B 64 LYS cc_start: 0.6897 (mmmt) cc_final: 0.6518 (mmtt) REVERT: B 104 ASP cc_start: 0.6658 (t0) cc_final: 0.6359 (t70) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.1822 time to fit residues: 19.5307 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 52 SER 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 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 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7439 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6203 Z= 0.213 Angle : 0.463 5.840 8415 Z= 0.251 Chirality : 0.041 0.136 911 Planarity : 0.003 0.037 1034 Dihedral : 7.829 86.512 980 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 1.61 (0.31), residues: 732 helix: 2.26 (0.29), residues: 325 sheet: 0.96 (0.41), residues: 151 loop : -0.42 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.012 0.001 PHE A 385 TYR 0.015 0.001 TYR C 106 ARG 0.004 0.000 ARG C 19 *********************** 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 to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.673 Fit side-chains REVERT: A 372 MET cc_start: 0.7565 (mmt) cc_final: 0.7231 (mmt) REVERT: B 64 LYS cc_start: 0.6962 (mmmt) cc_final: 0.6554 (mmtt) outliers start: 15 outliers final: 14 residues processed: 78 average time/residue: 0.1742 time to fit residues: 19.0898 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 52 SER 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 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 46 GLU 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: 0.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6203 Z= 0.220 Angle : 0.467 6.072 8415 Z= 0.254 Chirality : 0.042 0.135 911 Planarity : 0.003 0.037 1034 Dihedral : 7.844 85.444 980 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 1.53 (0.31), residues: 732 helix: 2.22 (0.28), residues: 325 sheet: 0.94 (0.41), residues: 150 loop : -0.50 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 PHE 0.012 0.001 PHE B 47 TYR 0.015 0.001 TYR C 106 ARG 0.004 0.001 ARG C 19 ********************** 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 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.621 Fit side-chains REVERT: A 372 MET cc_start: 0.7561 (mmt) cc_final: 0.7218 (mmt) REVERT: B 64 LYS cc_start: 0.6862 (mmmt) cc_final: 0.6471 (mmtt) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1731 time to fit residues: 18.2133 Evaluate side-chains 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 52 SER 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 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 46 GLU 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: 0.5980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.137983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110453 restraints weight = 16255.355| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.27 r_work: 0.3259 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6203 Z= 0.116 Angle : 0.422 6.156 8415 Z= 0.228 Chirality : 0.040 0.124 911 Planarity : 0.003 0.040 1034 Dihedral : 7.471 89.562 980 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.58 % Allowed : 12.04 % 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: 1.78 (0.31), residues: 732 helix: 2.54 (0.29), residues: 319 sheet: 1.01 (0.42), residues: 149 loop : -0.43 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 351 HIS 0.001 0.000 HIS A 195 PHE 0.010 0.001 PHE A 49 TYR 0.015 0.001 TYR C 106 ARG 0.006 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.72 seconds wall clock time: 30 minutes 13.96 seconds (1813.96 seconds total)