Starting phenix.real_space_refine on Sun Mar 10 15:59:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dep_27394/03_2024/8dep_27394_updated.pdb" } resolution = 3.6 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= 0.034 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 7 5.16 5 C 2175 2.51 5 N 489 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3223 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3223 Unusual residues: {'AJP': 4} Classifications: {'peptide': 398, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 384, None: 4} Not linked: pdbres="GLN A 459 " pdbres="AJP A 701 " Not linked: pdbres="AJP A 701 " pdbres="AJP A 702 " Not linked: pdbres="AJP A 702 " pdbres="AJP A 703 " Not linked: pdbres="AJP A 703 " pdbres="AJP A 704 " Chain breaks: 1 Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 530 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 2.48, per 1000 atoms: 0.77 Number of scatterers: 3223 At special positions: 0 Unit cell: (74.52, 69.12, 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 7 16.00 O 552 8.00 N 489 7.00 C 2175 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: 1.37 Conformation dependent library (CDL) restraints added in 697.5 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.896A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 68 through 89 removed outlier: 3.723A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 116 through 143 removed outlier: 3.620A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.922A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 3.616A pdb=" N ALA A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.714A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.936A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 3.680A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 355 removed outlier: 3.548A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 390 removed outlier: 3.924A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 378 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.909A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 3.965A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 458 removed outlier: 3.561A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 597 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: 0.84 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 911 1.35 - 1.46: 916 1.46 - 1.58: 1491 1.58 - 1.69: 4 1.69 - 1.81: 11 Bond restraints: 3333 Sorted by residual: bond pdb=" C23 AJP A 703 " pdb=" C24 AJP A 703 " ideal model delta sigma weight residual 1.522 1.610 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C23 AJP A 702 " pdb=" C24 AJP A 702 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C05 AJP A 704 " pdb=" C06 AJP A 704 " ideal model delta sigma weight residual 1.534 1.449 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 701 " pdb=" C24 AJP A 701 " ideal model delta sigma weight residual 1.522 1.607 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 704 " pdb=" C24 AJP A 704 " ideal model delta sigma weight residual 1.522 1.606 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.90: 81 105.90 - 112.93: 1962 112.93 - 119.95: 1081 119.95 - 126.98: 1447 126.98 - 134.01: 44 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 111.02 114.67 -3.65 1.22e+00 6.72e-01 8.95e+00 angle pdb=" N ILE A 41 " pdb=" CA ILE A 41 " pdb=" C ILE A 41 " ideal model delta sigma weight residual 106.55 110.75 -4.20 1.45e+00 4.76e-01 8.40e+00 angle pdb=" C ILE A 41 " pdb=" CA ILE A 41 " pdb=" CB ILE A 41 " ideal model delta sigma weight residual 112.68 109.72 2.96 1.14e+00 7.69e-01 6.74e+00 angle pdb=" C07 AJP A 701 " pdb=" C06 AJP A 701 " pdb=" C83 AJP A 701 " ideal model delta sigma weight residual 114.76 107.88 6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 111.82 114.30 -2.48 1.16e+00 7.43e-01 4.59e+00 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 2153 32.18 - 64.37: 52 64.37 - 96.55: 20 96.55 - 128.73: 13 128.73 - 160.91: 2 Dihedral angle restraints: 2240 sinusoidal: 1069 harmonic: 1171 Sorted by residual: dihedral pdb=" O31 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual 177.28 -21.81 -160.91 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C29 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual -60.96 98.67 -159.63 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C02 AJP A 703 " pdb=" C85 AJP A 703 " pdb=" O84 AJP A 703 " pdb=" C05 AJP A 703 " ideal model delta sinusoidal sigma weight residual -57.60 62.65 -120.25 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 512 0.070 - 0.140: 39 0.140 - 0.210: 15 0.210 - 0.280: 11 0.280 - 0.350: 9 Chirality restraints: 586 Sorted by residual: chirality pdb=" C11 AJP A 702 " pdb=" C10 AJP A 702 " pdb=" C12 AJP A 702 " pdb=" C16 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.20 2.55 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C19 AJP A 702 " pdb=" C18 AJP A 702 " pdb=" C20 AJP A 702 " pdb=" C24 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C23 AJP A 703 " pdb=" C22 AJP A 703 " pdb=" C24 AJP A 703 " pdb=" O25 AJP A 703 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 583 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 94 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 82 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 43 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 289 2.74 - 3.28: 3619 3.28 - 3.82: 5368 3.82 - 4.36: 5594 4.36 - 4.90: 9835 Nonbonded interactions: 24705 Sorted by model distance: nonbonded pdb=" O ALA A 135 " pdb=" OG SER A 138 " model vdw 2.197 2.440 nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.221 2.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.350 2.440 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.410 2.440 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.424 2.440 ... (remaining 24700 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: 0.340 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: 1.760 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 0.088 3333 Z= 0.516 Angle : 0.764 6.883 4615 Z= 0.347 Chirality : 0.067 0.350 586 Planarity : 0.005 0.065 521 Dihedral : 19.701 160.914 1488 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.65 % Allowed : 8.09 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.41), residues: 394 helix: 2.57 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -0.49 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.008 0.001 PHE A 326 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 268 *********************** 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 120 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.356 Fit side-chains REVERT: A 45 GLU cc_start: 0.8175 (tt0) cc_final: 0.7965 (tt0) REVERT: A 75 SER cc_start: 0.9174 (m) cc_final: 0.8962 (t) REVERT: A 287 TYR cc_start: 0.8052 (m-80) cc_final: 0.7788 (m-10) REVERT: A 293 ASN cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: A 294 GLU cc_start: 0.7821 (tp30) cc_final: 0.7316 (tp30) REVERT: A 306 ASN cc_start: 0.8570 (m-40) cc_final: 0.8217 (t0) REVERT: A 310 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t70) REVERT: A 316 LEU cc_start: 0.8900 (tp) cc_final: 0.8699 (tt) REVERT: A 346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0) REVERT: A 361 SER cc_start: 0.8810 (m) cc_final: 0.8587 (t) REVERT: A 412 THR cc_start: 0.8790 (m) cc_final: 0.8456 (m) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.1257 time to fit residues: 18.5419 Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3333 Z= 0.183 Angle : 0.647 7.888 4615 Z= 0.297 Chirality : 0.037 0.170 586 Planarity : 0.005 0.051 521 Dihedral : 11.754 123.602 892 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.24 % Allowed : 18.77 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.42), residues: 394 helix: 2.49 (0.27), residues: 325 sheet: None (None), residues: 0 loop : -0.33 (0.83), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.008 0.002 HIS A 355 PHE 0.020 0.001 PHE A 141 TYR 0.015 0.002 TYR A 149 ARG 0.001 0.000 ARG A 42 *********************** 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 107 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.368 Fit side-chains REVERT: A 45 GLU cc_start: 0.8227 (tt0) cc_final: 0.8003 (tt0) REVERT: A 123 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 181 SER cc_start: 0.8998 (m) cc_final: 0.8502 (p) REVERT: A 287 TYR cc_start: 0.8060 (m-80) cc_final: 0.7830 (m-10) REVERT: A 293 ASN cc_start: 0.8585 (t0) cc_final: 0.8342 (t0) REVERT: A 294 GLU cc_start: 0.7816 (tp30) cc_final: 0.7426 (tp30) REVERT: A 310 ASP cc_start: 0.8899 (t0) cc_final: 0.8639 (t0) REVERT: A 316 LEU cc_start: 0.8871 (tp) cc_final: 0.8647 (tt) REVERT: A 346 GLN cc_start: 0.8737 (mt0) cc_final: 0.8288 (mt0) REVERT: A 361 SER cc_start: 0.8783 (m) cc_final: 0.8534 (t) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1217 time to fit residues: 15.3333 Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3333 Z= 0.212 Angle : 0.589 6.483 4615 Z= 0.278 Chirality : 0.035 0.114 586 Planarity : 0.004 0.047 521 Dihedral : 7.383 60.999 892 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.24 % Allowed : 22.98 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.42), residues: 394 helix: 2.46 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.39 (0.76), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.007 0.001 HIS A 355 PHE 0.016 0.001 PHE A 141 TYR 0.012 0.001 TYR A 35 ARG 0.006 0.000 ARG A 133 *********************** 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 95 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.331 Fit side-chains REVERT: A 45 GLU cc_start: 0.8287 (tt0) cc_final: 0.8005 (tt0) REVERT: A 181 SER cc_start: 0.9013 (m) cc_final: 0.8547 (p) REVERT: A 277 ASN cc_start: 0.8758 (m-40) cc_final: 0.8465 (m110) REVERT: A 287 TYR cc_start: 0.8264 (m-80) cc_final: 0.7852 (m-10) REVERT: A 293 ASN cc_start: 0.8599 (t0) cc_final: 0.8145 (t0) REVERT: A 346 GLN cc_start: 0.8738 (mt0) cc_final: 0.8353 (mt0) REVERT: A 393 LYS cc_start: 0.8700 (tppt) cc_final: 0.8424 (tptp) REVERT: A 411 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8647 (ttpp) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.1242 time to fit residues: 13.8870 Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.003 0.026 3333 Z= 0.171 Angle : 0.547 7.395 4615 Z= 0.261 Chirality : 0.034 0.127 586 Planarity : 0.004 0.045 521 Dihedral : 5.958 53.715 892 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.24 % Allowed : 25.24 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.43), residues: 394 helix: 2.40 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.62 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.007 0.001 HIS A 355 PHE 0.010 0.001 PHE A 141 TYR 0.019 0.001 TYR A 149 ARG 0.005 0.000 ARG A 133 *********************** 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 97 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.346 Fit side-chains REVERT: A 45 GLU cc_start: 0.8219 (tt0) cc_final: 0.7938 (tt0) REVERT: A 122 MET cc_start: 0.8503 (tmm) cc_final: 0.8211 (tmm) REVERT: A 141 PHE cc_start: 0.8680 (t80) cc_final: 0.8465 (t80) REVERT: A 181 SER cc_start: 0.9032 (m) cc_final: 0.8536 (p) REVERT: A 277 ASN cc_start: 0.8775 (m-40) cc_final: 0.8422 (m110) REVERT: A 287 TYR cc_start: 0.8188 (m-80) cc_final: 0.7824 (m-10) REVERT: A 293 ASN cc_start: 0.8512 (t0) cc_final: 0.8282 (t0) REVERT: A 346 GLN cc_start: 0.8682 (mt0) cc_final: 0.8206 (mt0) REVERT: A 411 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8483 (ttpp) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.1261 time to fit residues: 14.7748 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3333 Z= 0.181 Angle : 0.541 6.958 4615 Z= 0.263 Chirality : 0.034 0.114 586 Planarity : 0.004 0.044 521 Dihedral : 5.529 53.858 892 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.59 % Allowed : 26.86 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.43), residues: 394 helix: 2.36 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.81 (0.72), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.010 0.001 PHE A 141 TYR 0.013 0.001 TYR A 149 ARG 0.004 0.000 ARG A 133 *********************** 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 93 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.371 Fit side-chains REVERT: A 45 GLU cc_start: 0.8224 (tt0) cc_final: 0.7935 (tt0) REVERT: A 172 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 181 SER cc_start: 0.9055 (m) cc_final: 0.8544 (p) REVERT: A 277 ASN cc_start: 0.8774 (m-40) cc_final: 0.8530 (m110) REVERT: A 287 TYR cc_start: 0.8245 (m-80) cc_final: 0.7997 (m-80) REVERT: A 293 ASN cc_start: 0.8491 (t0) cc_final: 0.8213 (t0) REVERT: A 346 GLN cc_start: 0.8671 (mt0) cc_final: 0.8248 (mt0) REVERT: A 363 TRP cc_start: 0.7528 (m-10) cc_final: 0.7184 (m-10) REVERT: A 411 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8589 (tttp) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.1222 time to fit residues: 13.8045 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3333 Z= 0.181 Angle : 0.531 7.178 4615 Z= 0.258 Chirality : 0.033 0.115 586 Planarity : 0.004 0.044 521 Dihedral : 5.379 53.818 892 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.59 % Allowed : 25.89 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.43), residues: 394 helix: 2.37 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.93 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.007 0.001 PHE A 416 TYR 0.023 0.001 TYR A 149 ARG 0.006 0.000 ARG A 133 *********************** 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 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8181 (tt0) cc_final: 0.7818 (tt0) REVERT: A 123 GLU cc_start: 0.7782 (tp30) cc_final: 0.7508 (tm-30) REVERT: A 181 SER cc_start: 0.9082 (m) cc_final: 0.8616 (p) REVERT: A 277 ASN cc_start: 0.8735 (m-40) cc_final: 0.8503 (m110) REVERT: A 287 TYR cc_start: 0.8198 (m-80) cc_final: 0.7953 (m-80) REVERT: A 346 GLN cc_start: 0.8636 (mt0) cc_final: 0.8225 (mt0) REVERT: A 363 TRP cc_start: 0.7412 (m-10) cc_final: 0.7116 (m-10) REVERT: A 411 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8530 (tttm) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.1282 time to fit residues: 13.4634 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3333 Z= 0.174 Angle : 0.523 7.423 4615 Z= 0.256 Chirality : 0.034 0.115 586 Planarity : 0.004 0.044 521 Dihedral : 5.320 53.295 892 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.27 % Allowed : 27.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.43), residues: 394 helix: 2.36 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.10 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.006 0.001 PHE A 141 TYR 0.020 0.001 TYR A 149 ARG 0.005 0.000 ARG A 133 *********************** 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 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8185 (tt0) cc_final: 0.7853 (tt0) REVERT: A 141 PHE cc_start: 0.8774 (t80) cc_final: 0.8180 (t80) REVERT: A 149 TYR cc_start: 0.7716 (t80) cc_final: 0.7239 (t80) REVERT: A 287 TYR cc_start: 0.8186 (m-80) cc_final: 0.7803 (m-10) REVERT: A 346 GLN cc_start: 0.8697 (mt0) cc_final: 0.8254 (mt0) REVERT: A 363 TRP cc_start: 0.7244 (m-10) cc_final: 0.6967 (m-10) REVERT: A 393 LYS cc_start: 0.8638 (tppt) cc_final: 0.8248 (tppt) REVERT: A 411 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8528 (tttm) outliers start: 7 outliers final: 7 residues processed: 84 average time/residue: 0.1191 time to fit residues: 12.6715 Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 overall best weight: 0.3432 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3333 Z= 0.156 Angle : 0.531 7.442 4615 Z= 0.257 Chirality : 0.033 0.114 586 Planarity : 0.004 0.044 521 Dihedral : 5.171 53.088 892 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.91 % Allowed : 26.86 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.43), residues: 394 helix: 2.40 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.08 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.005 0.001 PHE A 141 TYR 0.015 0.001 TYR A 149 ARG 0.006 0.000 ARG A 133 *********************** 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: 9 poor density : 85 time to evaluate : 0.341 Fit side-chains REVERT: A 45 GLU cc_start: 0.8152 (tt0) cc_final: 0.7823 (tt0) REVERT: A 141 PHE cc_start: 0.8730 (t80) cc_final: 0.7957 (t80) REVERT: A 149 TYR cc_start: 0.7584 (t80) cc_final: 0.7108 (t80) REVERT: A 287 TYR cc_start: 0.8139 (m-80) cc_final: 0.7662 (m-10) REVERT: A 336 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7461 (mmtt) REVERT: A 363 TRP cc_start: 0.7230 (m-10) cc_final: 0.6935 (m-10) REVERT: A 393 LYS cc_start: 0.8602 (tppt) cc_final: 0.8187 (tppt) REVERT: A 411 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8503 (tttm) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.1251 time to fit residues: 13.6494 Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3333 Z= 0.155 Angle : 0.541 7.805 4615 Z= 0.260 Chirality : 0.033 0.113 586 Planarity : 0.004 0.044 521 Dihedral : 5.060 52.411 892 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.59 % Allowed : 28.16 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.43), residues: 394 helix: 2.35 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.11 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.006 0.001 PHE A 276 TYR 0.024 0.001 TYR A 286 ARG 0.006 0.000 ARG A 133 *********************** 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: 8 poor density : 87 time to evaluate : 0.351 Fit side-chains REVERT: A 45 GLU cc_start: 0.8143 (tt0) cc_final: 0.7809 (tt0) REVERT: A 125 PHE cc_start: 0.9022 (m-80) cc_final: 0.8684 (m-80) REVERT: A 141 PHE cc_start: 0.8787 (t80) cc_final: 0.7909 (t80) REVERT: A 149 TYR cc_start: 0.7582 (t80) cc_final: 0.7080 (t80) REVERT: A 287 TYR cc_start: 0.8126 (m-80) cc_final: 0.7709 (m-10) REVERT: A 363 TRP cc_start: 0.7183 (m-10) cc_final: 0.6737 (m-10) REVERT: A 366 TYR cc_start: 0.8388 (m-80) cc_final: 0.7921 (m-80) REVERT: A 393 LYS cc_start: 0.8484 (tppt) cc_final: 0.8163 (tppt) REVERT: A 411 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8573 (tttp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1222 time to fit residues: 14.2049 Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3333 Z= 0.170 Angle : 0.556 9.060 4615 Z= 0.264 Chirality : 0.034 0.114 586 Planarity : 0.004 0.043 521 Dihedral : 5.028 51.793 892 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.29 % Allowed : 29.45 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.43), residues: 394 helix: 2.34 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.10 (0.70), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.002 0.000 HIS A 27 PHE 0.006 0.001 PHE A 103 TYR 0.016 0.001 TYR A 286 ARG 0.007 0.000 ARG A 133 ********************** 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 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8148 (tt0) cc_final: 0.7813 (tt0) REVERT: A 125 PHE cc_start: 0.9018 (m-80) cc_final: 0.8793 (m-80) REVERT: A 141 PHE cc_start: 0.8901 (t80) cc_final: 0.8032 (t80) REVERT: A 149 TYR cc_start: 0.7589 (t80) cc_final: 0.7092 (t80) REVERT: A 287 TYR cc_start: 0.8203 (m-80) cc_final: 0.7765 (m-10) REVERT: A 363 TRP cc_start: 0.7233 (m-10) cc_final: 0.6820 (m-10) REVERT: A 366 TYR cc_start: 0.8376 (m-80) cc_final: 0.7921 (m-80) REVERT: A 393 LYS cc_start: 0.8474 (tppt) cc_final: 0.8151 (tppt) REVERT: A 411 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8688 (tttp) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1296 time to fit residues: 13.7582 Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 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 293 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.121618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108272 restraints weight = 5793.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111758 restraints weight = 2469.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114019 restraints weight = 1342.248| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3333 Z= 0.212 Angle : 0.578 9.080 4615 Z= 0.279 Chirality : 0.035 0.119 586 Planarity : 0.004 0.043 521 Dihedral : 5.165 50.908 892 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.29 % Allowed : 29.45 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.43), residues: 394 helix: 2.25 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.09 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.002 0.000 HIS A 27 PHE 0.005 0.001 PHE A 416 TYR 0.017 0.001 TYR A 286 ARG 0.007 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1046.74 seconds wall clock time: 19 minutes 40.63 seconds (1180.63 seconds total)