Starting phenix.real_space_refine on Mon Sep 23 15:56:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/09_2024/7tx6_26155.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2122 2.51 5 N 503 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3169 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 10, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 1, 'MTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MTX:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.80, per 1000 atoms: 0.88 Number of scatterers: 3169 At special positions: 0 Unit cell: (72.36, 61.56, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 534 8.00 N 503 7.00 C 2122 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 - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 375.4 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A2644 " Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 4.105A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.835A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.986A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 3.861A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.562A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.906A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.538A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.616A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.936A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.511A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 326 removed outlier: 4.015A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 328 No H-bonds generated for 'chain 'A' and resid 327 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.097A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 389 removed outlier: 3.702A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.726A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 459 removed outlier: 3.664A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 714 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: 0.89 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 446 1.31 - 1.43: 993 1.43 - 1.56: 1806 1.56 - 1.68: 5 1.68 - 1.81: 15 Bond restraints: 3265 Sorted by residual: bond pdb=" C VAL A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.449 -0.114 1.31e-02 5.83e+03 7.53e+01 bond pdb=" C4 MTX A2644 " pdb=" NA4 MTX A2644 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MTX A2644 " pdb=" C MTX A2644 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C2 MTX A2644 " pdb=" NA2 MTX A2644 " ideal model delta sigma weight residual 1.341 1.451 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C14 MTX A2644 " pdb=" N10 MTX A2644 " ideal model delta sigma weight residual 1.368 1.453 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4147 1.56 - 3.11: 237 3.11 - 4.67: 79 4.67 - 6.23: 13 6.23 - 7.79: 4 Bond angle restraints: 4480 Sorted by residual: angle pdb=" C VAL A 410 " pdb=" N LYS A 411 " pdb=" CA LYS A 411 " ideal model delta sigma weight residual 120.28 114.07 6.21 1.34e+00 5.57e-01 2.15e+01 angle pdb=" CA ILE A 48 " pdb=" C ILE A 48 " pdb=" O ILE A 48 " ideal model delta sigma weight residual 121.17 116.45 4.72 1.06e+00 8.90e-01 1.98e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 120.85 116.34 4.51 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.57 116.30 4.27 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N PHE A 416 " pdb=" CA PHE A 416 " pdb=" C PHE A 416 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 ... (remaining 4475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 1837 24.23 - 48.46: 81 48.46 - 72.69: 7 72.69 - 96.92: 8 96.92 - 121.14: 7 Dihedral angle restraints: 1940 sinusoidal: 769 harmonic: 1171 Sorted by residual: dihedral pdb=" C02 AJP A2501 " pdb=" C85 AJP A2501 " pdb=" O84 AJP A2501 " pdb=" C05 AJP A2501 " ideal model delta sinusoidal sigma weight residual -57.60 63.54 -121.14 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C28 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O31 AJP A2501 " ideal model delta sinusoidal sigma weight residual -54.31 65.16 -119.47 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O31 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O78 AJP A2501 " ideal model delta sinusoidal sigma weight residual 175.34 56.37 118.97 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 469 0.070 - 0.141: 50 0.141 - 0.211: 12 0.211 - 0.281: 6 0.281 - 0.352: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" C11 AJP A2501 " pdb=" C10 AJP A2501 " pdb=" C12 AJP A2501 " pdb=" C16 AJP A2501 " both_signs ideal model delta sigma weight residual False 2.20 2.56 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C15 AJP A2501 " pdb=" C14 AJP A2501 " pdb=" C16 AJP A2501 " pdb=" C20 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.42 -2.70 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C23 AJP A2501 " pdb=" C22 AJP A2501 " pdb=" C24 AJP A2501 " pdb=" O25 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 62 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLU A 62 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU A 62 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 63 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 94 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 68 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE A 68 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1092 2.84 - 3.36: 3421 3.36 - 3.87: 5070 3.87 - 4.39: 5536 4.39 - 4.90: 9405 Nonbonded interactions: 24524 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" N SER A 301 " model vdw 2.327 3.120 nonbonded pdb=" OD1 ASP A 56 " pdb=" N LYS A 57 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 102 " pdb=" OG SER A 105 " model vdw 2.421 3.040 nonbonded pdb=" O LEU A 440 " pdb=" OG SER A 443 " model vdw 2.482 3.040 nonbonded pdb=" O THR A 87 " pdb=" O LEU A 90 " model vdw 2.484 3.040 ... (remaining 24519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 0.121 3265 Z= 0.491 Angle : 0.902 7.786 4480 Z= 0.564 Chirality : 0.055 0.352 538 Planarity : 0.005 0.071 529 Dihedral : 17.014 121.145 1188 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 6.88 % Favored : 92.50 % Cbeta Deviations : 0.27 % 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: 2.51 (0.42), residues: 394 helix: 2.27 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.83 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 355 PHE 0.010 0.001 PHE A 405 TYR 0.013 0.001 TYR A 438 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 282 TYR cc_start: 0.8319 (m-80) cc_final: 0.8030 (m-10) REVERT: A 287 TYR cc_start: 0.8372 (m-80) cc_final: 0.7722 (m-80) REVERT: A 363 TRP cc_start: 0.2795 (m100) cc_final: 0.2102 (m100) REVERT: A 395 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7789 (tt) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1501 time to fit residues: 18.8783 Evaluate side-chains 94 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.196 Angle : 0.662 8.553 4480 Z= 0.315 Chirality : 0.039 0.176 538 Planarity : 0.004 0.064 529 Dihedral : 9.241 73.889 571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.56 % Allowed : 15.94 % Favored : 82.50 % Cbeta Deviations : 0.27 % 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: 3.22 (0.43), residues: 394 helix: 2.67 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.51 (0.81), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.002 0.001 HIS A 114 PHE 0.012 0.001 PHE A 432 TYR 0.013 0.001 TYR A 305 ARG 0.002 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.332 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.1263 time to fit residues: 14.7319 Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3265 Z= 0.178 Angle : 0.585 7.226 4480 Z= 0.285 Chirality : 0.037 0.120 538 Planarity : 0.004 0.060 529 Dihedral : 7.544 85.144 569 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.94 % Allowed : 22.19 % Favored : 76.88 % Cbeta Deviations : 0.27 % 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: 3.17 (0.43), residues: 394 helix: 2.74 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.00 (0.77), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.011 0.001 PHE A 34 TYR 0.014 0.001 TYR A 305 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7717 (ptt180) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.1420 time to fit residues: 15.6041 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3265 Z= 0.346 Angle : 0.674 9.204 4480 Z= 0.346 Chirality : 0.040 0.120 538 Planarity : 0.004 0.058 529 Dihedral : 7.637 89.058 569 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.12 % Allowed : 22.81 % Favored : 74.06 % Cbeta Deviations : 0.27 % 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: 2.70 (0.42), residues: 394 helix: 2.40 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.77 (0.76), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 334 HIS 0.006 0.002 HIS A 358 PHE 0.011 0.002 PHE A 165 TYR 0.016 0.002 TYR A 438 ARG 0.003 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8324 (tt0) REVERT: A 119 MET cc_start: 0.8196 (mmm) cc_final: 0.7958 (mmm) REVERT: A 172 GLN cc_start: 0.8717 (tp40) cc_final: 0.8292 (tp-100) REVERT: A 444 ILE cc_start: 0.8629 (tt) cc_final: 0.8310 (tp) REVERT: A 451 MET cc_start: 0.7285 (tmm) cc_final: 0.6851 (tmm) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 0.1355 time to fit residues: 15.4798 Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.217 Angle : 0.597 7.057 4480 Z= 0.298 Chirality : 0.036 0.120 538 Planarity : 0.004 0.057 529 Dihedral : 7.422 85.867 569 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.19 % Allowed : 24.69 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 2.86 (0.43), residues: 394 helix: 2.47 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -0.81 (0.82), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.010 0.001 PHE A 165 TYR 0.012 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8267 (tt0) REVERT: A 119 MET cc_start: 0.8206 (mmm) cc_final: 0.7850 (mmm) REVERT: A 133 ARG cc_start: 0.8232 (ttp-170) cc_final: 0.7794 (ptt180) REVERT: A 451 MET cc_start: 0.7520 (tmm) cc_final: 0.7279 (tmm) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1379 time to fit residues: 15.3642 Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3265 Z= 0.193 Angle : 0.580 7.585 4480 Z= 0.285 Chirality : 0.036 0.118 538 Planarity : 0.004 0.056 529 Dihedral : 7.285 82.863 569 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.50 % Allowed : 24.69 % Favored : 72.81 % Cbeta Deviations : 0.27 % 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: 3.07 (0.44), residues: 394 helix: 2.59 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -0.64 (0.85), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.010 0.001 PHE A 34 TYR 0.011 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8254 (tt0) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.1394 time to fit residues: 15.9556 Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.7494 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3265 Z= 0.170 Angle : 0.592 10.837 4480 Z= 0.281 Chirality : 0.035 0.113 538 Planarity : 0.004 0.055 529 Dihedral : 7.386 84.349 569 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.88 % Allowed : 25.00 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.23 (0.43), residues: 394 helix: 2.70 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.67 (0.85), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.009 0.001 PHE A 165 TYR 0.010 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7959 (tt0) REVERT: A 102 SER cc_start: 0.8983 (m) cc_final: 0.8483 (p) REVERT: A 133 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7794 (ptt180) REVERT: A 394 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8458 (tm-30) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.1508 time to fit residues: 16.8601 Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3265 Z= 0.188 Angle : 0.592 10.551 4480 Z= 0.285 Chirality : 0.035 0.115 538 Planarity : 0.004 0.055 529 Dihedral : 7.366 83.609 569 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.50 % Allowed : 24.06 % Favored : 73.44 % Cbeta Deviations : 0.27 % 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: 3.27 (0.44), residues: 394 helix: 2.71 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.48 (0.86), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.011 0.001 PHE A 34 TYR 0.010 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7946 (tt0) REVERT: A 102 SER cc_start: 0.8992 (m) cc_final: 0.8493 (p) REVERT: A 133 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7890 (ptt180) REVERT: A 394 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 395 LEU cc_start: 0.7212 (mt) cc_final: 0.6824 (mt) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.1399 time to fit residues: 15.6599 Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7505 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3265 Z= 0.192 Angle : 0.630 11.779 4480 Z= 0.294 Chirality : 0.035 0.116 538 Planarity : 0.004 0.055 529 Dihedral : 7.358 83.339 569 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.81 % Allowed : 24.06 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.26 (0.44), residues: 394 helix: 2.71 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.59 (0.86), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.013 0.001 PHE A 195 TYR 0.010 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8689 (tm-30) cc_final: 0.7951 (tt0) REVERT: A 102 SER cc_start: 0.8983 (m) cc_final: 0.8494 (p) REVERT: A 119 MET cc_start: 0.8058 (mmm) cc_final: 0.7789 (mmm) REVERT: A 133 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7895 (ptt180) REVERT: A 358 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6123 (t-90) REVERT: A 394 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 395 LEU cc_start: 0.7144 (mt) cc_final: 0.6726 (mt) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.1361 time to fit residues: 15.3763 Evaluate side-chains 92 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7488 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3265 Z= 0.178 Angle : 0.639 11.173 4480 Z= 0.294 Chirality : 0.035 0.112 538 Planarity : 0.004 0.055 529 Dihedral : 7.350 84.684 569 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.50 % Allowed : 24.38 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.34 (0.43), residues: 394 helix: 2.77 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.62 (0.85), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 270 HIS 0.002 0.001 HIS A 358 PHE 0.012 0.001 PHE A 34 TYR 0.009 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.8951 (m) cc_final: 0.8518 (p) REVERT: A 119 MET cc_start: 0.8066 (mmm) cc_final: 0.7814 (mmm) REVERT: A 133 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7915 (ptt180) REVERT: A 358 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6162 (t-90) REVERT: A 394 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 395 LEU cc_start: 0.7184 (mt) cc_final: 0.6725 (mt) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1534 time to fit residues: 16.9044 Evaluate side-chains 92 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.143480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132307 restraints weight = 5237.776| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.53 r_work: 0.3540 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3265 Z= 0.158 Angle : 0.624 10.928 4480 Z= 0.285 Chirality : 0.034 0.110 538 Planarity : 0.004 0.055 529 Dihedral : 7.187 84.097 569 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 25.00 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.44 (0.44), residues: 394 helix: 2.79 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -0.47 (0.86), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 270 HIS 0.001 0.000 HIS A 358 PHE 0.035 0.001 PHE A 322 TYR 0.008 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1075.12 seconds wall clock time: 19 minutes 36.70 seconds (1176.70 seconds total)