Starting phenix.real_space_refine on Mon Mar 11 15:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p15_13156/03_2024/7p15_13156_updated.pdb" } resolution = 3.58 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 14 5.16 5 C 5451 2.51 5 N 1439 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8587 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 515} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3398 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLN%COO:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 716 Unusual residues: {'4OI': 1} Classifications: {'DNA': 32, 'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 33, None: 1} Not linked: pdbres=" DG F 32 " pdbres="4OI F 101 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.29, per 1000 atoms: 0.62 Number of scatterers: 8587 At special positions: 0 Unit cell: (95.06, 104.76, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 34 15.00 O 1649 8.00 N 1439 7.00 C 5451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 33.3% alpha, 10.6% beta 12 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 removed outlier: 3.712A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.300A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.861A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 508 removed outlier: 4.191A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 505 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.695A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.831A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 4.054A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.710A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 364 through 382 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.641A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.802A pdb=" N LEU A 74 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= D, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= E, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.725A pdb=" N GLN A 330 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 439 through 441 removed outlier: 8.737A pdb=" N PHE A 440 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN A 494 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.531A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 447 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 457 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 61 through 64 Processing sheet with id= I, first strand: chain 'B' and resid 232 through 234 removed outlier: 4.119A pdb=" N TYR B 232 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 187 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.968A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 337 through 342 removed outlier: 3.640A pdb=" N GLN B 330 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 328 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 388 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE B 329 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 390 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS B 331 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1379 1.32 - 1.44: 2448 1.44 - 1.56: 4961 1.56 - 1.69: 68 1.69 - 1.81: 26 Bond restraints: 8882 Sorted by residual: bond pdb=" O3' DC F 15 " pdb=" P DT F 16 " ideal model delta sigma weight residual 1.607 1.480 0.127 1.50e-02 4.44e+03 7.19e+01 bond pdb=" C5 OMC F 4 " pdb=" C6 OMC F 4 " ideal model delta sigma weight residual 1.488 1.342 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 OMC F 4 " pdb=" N3 OMC F 4 " ideal model delta sigma weight residual 1.491 1.349 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C2 OMC F 2 " pdb=" N3 OMC F 2 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" N3 OMC F 4 " pdb=" C4 OMC F 4 " ideal model delta sigma weight residual 1.448 1.315 0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 8877 not shown) Histogram of bond angle deviations from ideal: 57.86 - 73.33: 3 73.33 - 88.79: 0 88.79 - 104.25: 276 104.25 - 119.71: 7742 119.71 - 135.17: 4194 Bond angle restraints: 12215 Sorted by residual: angle pdb=" C5' DA F 21 " pdb=" C4' DA F 21 " pdb=" O4' DA F 21 " ideal model delta sigma weight residual 109.40 127.10 -17.70 1.50e+00 4.44e-01 1.39e+02 angle pdb=" C3' DC F 15 " pdb=" O3' DC F 15 " pdb=" P DT F 16 " ideal model delta sigma weight residual 120.20 132.96 -12.76 1.50e+00 4.44e-01 7.24e+01 angle pdb=" N ASP B 186 " pdb=" CA ASP B 186 " pdb=" C ASP B 186 " ideal model delta sigma weight residual 109.24 120.86 -11.62 1.63e+00 3.76e-01 5.08e+01 angle pdb=" C5' DC F 20 " pdb=" C4' DC F 20 " pdb=" O4' DC F 20 " ideal model delta sigma weight residual 109.40 119.52 -10.12 1.50e+00 4.44e-01 4.55e+01 angle pdb=" C5' DC F 22 " pdb=" C4' DC F 22 " pdb=" O4' DC F 22 " ideal model delta sigma weight residual 109.40 118.85 -9.45 1.50e+00 4.44e-01 3.97e+01 ... (remaining 12210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4541 17.94 - 35.89: 533 35.89 - 53.83: 133 53.83 - 71.78: 30 71.78 - 89.72: 11 Dihedral angle restraints: 5248 sinusoidal: 2417 harmonic: 2831 Sorted by residual: dihedral pdb=" C TYR A 181 " pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" CB TYR A 181 " ideal model delta harmonic sigma weight residual -122.60 -109.61 -12.99 0 2.50e+00 1.60e-01 2.70e+01 dihedral pdb=" C GLU B 169 " pdb=" N GLU B 169 " pdb=" CA GLU B 169 " pdb=" CB GLU B 169 " ideal model delta harmonic sigma weight residual -122.60 -132.60 10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CA GLU B 344 " pdb=" C GLU B 344 " pdb=" N PRO B 345 " pdb=" CA PRO B 345 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 1296 0.157 - 0.314: 23 0.314 - 0.471: 9 0.471 - 0.628: 2 0.628 - 0.785: 1 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C4' DA F 21 " pdb=" C5' DA F 21 " pdb=" O4' DA F 21 " pdb=" C3' DA F 21 " both_signs ideal model delta sigma weight residual False -2.53 -1.74 -0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C4' DC F 20 " pdb=" C5' DC F 20 " pdb=" O4' DC F 20 " pdb=" C3' DC F 20 " both_signs ideal model delta sigma weight residual False -2.53 -1.96 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" C4' DC F 22 " pdb=" C5' DC F 22 " pdb=" O4' DC F 22 " pdb=" C3' DC F 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.01 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 1328 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC F 4 " 0.041 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' OMC F 4 " 0.447 2.00e-02 2.50e+03 pdb=" O4' OMC F 4 " 0.700 2.00e-02 2.50e+03 pdb=" C3' OMC F 4 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMC F 4 " -0.615 2.00e-02 2.50e+03 pdb=" C2' OMC F 4 " -0.202 2.00e-02 2.50e+03 pdb=" O2' OMC F 4 " 0.942 2.00e-02 2.50e+03 pdb=" C1' OMC F 4 " 0.206 2.00e-02 2.50e+03 pdb=" N1 OMC F 4 " -0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC F 2 " -0.027 2.00e-02 2.50e+03 5.40e-01 6.55e+03 pdb=" C4' OMC F 2 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMC F 2 " 0.561 2.00e-02 2.50e+03 pdb=" C3' OMC F 2 " -0.564 2.00e-02 2.50e+03 pdb=" O3' OMC F 2 " -0.519 2.00e-02 2.50e+03 pdb=" C2' OMC F 2 " -0.206 2.00e-02 2.50e+03 pdb=" O2' OMC F 2 " 0.856 2.00e-02 2.50e+03 pdb=" C1' OMC F 2 " 0.271 2.00e-02 2.50e+03 pdb=" N1 OMC F 2 " -0.819 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 78 " 0.540 9.50e-02 1.11e+02 2.42e-01 3.58e+01 pdb=" NE ARG A 78 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 78 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 78 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 78 " 0.018 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 846 2.74 - 3.28: 8119 3.28 - 3.82: 14321 3.82 - 4.36: 16702 4.36 - 4.90: 28294 Nonbonded interactions: 68282 Sorted by model distance: nonbonded pdb=" O LEU B 80 " pdb=" OG1 THR B 84 " model vdw 2.202 2.440 nonbonded pdb=" OD1 ASP B 17 " pdb=" OH TYR B 56 " model vdw 2.245 2.440 nonbonded pdb=" O LEU A 486 " pdb=" NZ LYS A 528 " model vdw 2.247 2.520 nonbonded pdb=" O LYS A 540 " pdb=" OG SER B 280 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 253 " pdb=" OD1 ASP B 256 " model vdw 2.290 2.440 ... (remaining 68277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.020 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.900 Find NCS groups from input model: 0.220 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.007 0.146 8882 Z= 0.421 Angle : 0.932 17.698 12215 Z= 0.555 Chirality : 0.071 0.785 1331 Planarity : 0.023 0.601 1422 Dihedral : 16.436 89.724 3422 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.23 % Allowed : 1.75 % Favored : 98.01 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.03 % 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: -1.15 (0.26), residues: 963 helix: 0.33 (0.27), residues: 352 sheet: -1.34 (0.45), residues: 132 loop : -1.40 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 414 HIS 0.003 0.001 HIS A 208 PHE 0.021 0.002 PHE A 77 TYR 0.027 0.002 TYR B 339 ARG 0.004 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 THR cc_start: 0.7879 (m) cc_final: 0.7417 (m) REVERT: A 232 TYR cc_start: 0.8293 (m-10) cc_final: 0.7963 (m-10) REVERT: A 537 PRO cc_start: 0.8730 (Cg_exo) cc_final: 0.8498 (Cg_endo) REVERT: B 22 LYS cc_start: 0.7901 (tttm) cc_final: 0.7601 (pttt) REVERT: B 185 ASP cc_start: 0.6693 (m-30) cc_final: 0.6230 (m-30) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.2280 time to fit residues: 39.1370 Evaluate side-chains 95 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 161 GLN A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8882 Z= 0.177 Angle : 0.694 15.080 12215 Z= 0.405 Chirality : 0.043 0.174 1331 Planarity : 0.006 0.112 1422 Dihedral : 15.343 72.244 1408 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.94 % Allowed : 7.60 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.27), residues: 963 helix: 1.15 (0.28), residues: 342 sheet: -1.18 (0.43), residues: 151 loop : -1.14 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 414 HIS 0.002 0.000 HIS B 208 PHE 0.011 0.001 PHE B 124 TYR 0.020 0.001 TYR A 319 ARG 0.005 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.860 Fit side-chains REVERT: A 10 VAL cc_start: 0.8291 (p) cc_final: 0.7903 (m) REVERT: A 339 TYR cc_start: 0.7387 (m-10) cc_final: 0.6917 (m-10) REVERT: B 22 LYS cc_start: 0.7897 (tttm) cc_final: 0.7612 (pttt) outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.2008 time to fit residues: 31.3186 Evaluate side-chains 97 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 161 GLN A 258 GLN A 306 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN B 258 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8882 Z= 0.402 Angle : 0.806 12.828 12215 Z= 0.453 Chirality : 0.047 0.154 1331 Planarity : 0.007 0.118 1422 Dihedral : 15.893 96.465 1406 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.46 % Allowed : 9.94 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 963 helix: 0.55 (0.28), residues: 341 sheet: -1.60 (0.42), residues: 150 loop : -1.29 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 402 HIS 0.004 0.001 HIS A 315 PHE 0.029 0.003 PHE A 160 TYR 0.024 0.002 TYR B 339 ARG 0.005 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.865 Fit side-chains REVERT: B 22 LYS cc_start: 0.7942 (tttm) cc_final: 0.7574 (pttt) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.1927 time to fit residues: 30.4794 Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 258 GLN A 330 GLN A 348 ASN B 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8882 Z= 0.156 Angle : 0.664 13.725 12215 Z= 0.389 Chirality : 0.042 0.149 1331 Planarity : 0.006 0.115 1422 Dihedral : 15.252 103.784 1406 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.75 % Allowed : 13.10 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.27), residues: 963 helix: 1.16 (0.29), residues: 341 sheet: -1.38 (0.42), residues: 151 loop : -1.01 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.010 0.001 PHE B 124 TYR 0.024 0.001 TYR A 501 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.991 Fit side-chains REVERT: A 339 TYR cc_start: 0.7403 (m-10) cc_final: 0.7058 (m-10) REVERT: B 22 LYS cc_start: 0.7919 (tttm) cc_final: 0.7544 (pttt) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 0.1866 time to fit residues: 31.4077 Evaluate side-chains 107 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 161 GLN A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8882 Z= 0.308 Angle : 0.733 13.105 12215 Z= 0.419 Chirality : 0.044 0.154 1331 Planarity : 0.007 0.118 1422 Dihedral : 15.538 104.574 1406 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.11 % Allowed : 14.50 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 963 helix: 0.91 (0.28), residues: 336 sheet: -1.51 (0.43), residues: 150 loop : -1.06 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 402 HIS 0.003 0.001 HIS A 221 PHE 0.020 0.002 PHE A 160 TYR 0.033 0.002 TYR A 501 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.919 Fit side-chains REVERT: A 229 TRP cc_start: 0.8231 (t60) cc_final: 0.7513 (t60) REVERT: B 22 LYS cc_start: 0.7939 (tttm) cc_final: 0.7565 (pttt) outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.1973 time to fit residues: 31.4032 Evaluate side-chains 103 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 161 GLN A 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8882 Z= 0.287 Angle : 0.722 13.133 12215 Z= 0.414 Chirality : 0.044 0.151 1331 Planarity : 0.007 0.117 1422 Dihedral : 15.522 103.098 1406 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 15.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 963 helix: 0.85 (0.28), residues: 336 sheet: -1.59 (0.43), residues: 150 loop : -1.11 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 212 HIS 0.003 0.001 HIS B 208 PHE 0.017 0.002 PHE A 160 TYR 0.024 0.002 TYR A 501 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.016 Fit side-chains REVERT: A 47 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7246 (pt) REVERT: A 92 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6776 (pp) REVERT: A 340 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: B 22 LYS cc_start: 0.7929 (tttm) cc_final: 0.7557 (pttt) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.1947 time to fit residues: 30.7001 Evaluate side-chains 109 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 161 GLN A 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8882 Z= 0.168 Angle : 0.658 13.157 12215 Z= 0.385 Chirality : 0.041 0.146 1331 Planarity : 0.006 0.116 1422 Dihedral : 15.174 99.782 1406 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.87 % Allowed : 16.49 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.28), residues: 963 helix: 1.36 (0.29), residues: 330 sheet: -1.25 (0.42), residues: 155 loop : -0.87 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 212 HIS 0.002 0.001 HIS A 208 PHE 0.014 0.001 PHE A 130 TYR 0.018 0.001 TYR A 501 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.831 Fit side-chains REVERT: A 92 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6755 (pp) REVERT: A 339 TYR cc_start: 0.7619 (m-10) cc_final: 0.7114 (m-10) REVERT: A 340 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: B 22 LYS cc_start: 0.7889 (tttm) cc_final: 0.7529 (pttt) REVERT: B 328 GLU cc_start: 0.7693 (mp0) cc_final: 0.7492 (mp0) outliers start: 16 outliers final: 9 residues processed: 118 average time/residue: 0.2213 time to fit residues: 37.6225 Evaluate side-chains 108 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 83 optimal weight: 0.2980 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8882 Z= 0.277 Angle : 0.718 12.949 12215 Z= 0.412 Chirality : 0.044 0.149 1331 Planarity : 0.006 0.117 1422 Dihedral : 15.422 101.454 1406 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.87 % Allowed : 17.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 963 helix: 1.08 (0.28), residues: 334 sheet: -1.36 (0.42), residues: 154 loop : -0.96 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 212 HIS 0.003 0.001 HIS A 208 PHE 0.017 0.002 PHE A 160 TYR 0.029 0.002 TYR A 232 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.948 Fit side-chains REVERT: A 340 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: B 22 LYS cc_start: 0.7925 (tttm) cc_final: 0.7561 (pttt) outliers start: 16 outliers final: 14 residues processed: 112 average time/residue: 0.1997 time to fit residues: 31.9306 Evaluate side-chains 110 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN A 258 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8882 Z= 0.217 Angle : 0.687 13.206 12215 Z= 0.398 Chirality : 0.043 0.146 1331 Planarity : 0.006 0.116 1422 Dihedral : 15.323 97.451 1406 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.22 % Allowed : 17.08 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.28), residues: 963 helix: 1.19 (0.29), residues: 334 sheet: -1.14 (0.44), residues: 142 loop : -0.95 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 212 HIS 0.003 0.001 HIS A 208 PHE 0.014 0.001 PHE A 130 TYR 0.023 0.002 TYR A 232 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.948 Fit side-chains REVERT: A 340 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: B 22 LYS cc_start: 0.7920 (tttm) cc_final: 0.7545 (pttt) REVERT: B 310 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7433 (mm) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 0.2026 time to fit residues: 32.1759 Evaluate side-chains 109 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.0050 chunk 24 optimal weight: 3.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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: 0.6996 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8882 Z= 0.169 Angle : 0.660 13.185 12215 Z= 0.386 Chirality : 0.041 0.146 1331 Planarity : 0.006 0.115 1422 Dihedral : 15.105 95.878 1406 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 17.89 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.28), residues: 963 helix: 1.29 (0.29), residues: 342 sheet: -0.99 (0.44), residues: 143 loop : -0.96 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 212 HIS 0.002 0.001 HIS B 208 PHE 0.018 0.001 PHE A 130 TYR 0.019 0.001 TYR A 501 ARG 0.008 0.000 ARG B 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.8105 (m-80) cc_final: 0.7841 (t80) REVERT: A 339 TYR cc_start: 0.7538 (m-10) cc_final: 0.6990 (m-10) REVERT: A 340 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: B 22 LYS cc_start: 0.7902 (tttm) cc_final: 0.7518 (pttt) REVERT: B 310 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7442 (mm) outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 0.2035 time to fit residues: 33.0073 Evaluate side-chains 112 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.205729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168821 restraints weight = 10026.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170831 restraints weight = 8267.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172839 restraints weight = 6617.285| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8882 Z= 0.201 Angle : 0.678 13.070 12215 Z= 0.394 Chirality : 0.042 0.149 1331 Planarity : 0.006 0.116 1422 Dihedral : 15.170 96.266 1406 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.87 % Allowed : 17.89 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.28), residues: 963 helix: 1.28 (0.29), residues: 341 sheet: -0.96 (0.44), residues: 142 loop : -0.99 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 212 HIS 0.002 0.001 HIS B 208 PHE 0.018 0.001 PHE A 130 TYR 0.020 0.002 TYR A 232 ARG 0.007 0.000 ARG B 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.70 seconds wall clock time: 30 minutes 17.06 seconds (1817.06 seconds total)