Starting phenix.real_space_refine on Tue Feb 13 09:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmv_32617/02_2024/7wmv_32617_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.155 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 41 5.16 5 C 3252 2.51 5 N 776 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4608 Classifications: {'peptide': 602} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'1YI': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.25, per 1000 atoms: 0.66 Number of scatterers: 4899 At special positions: 0 Unit cell: (91.131, 73.89, 84.563, 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 41 16.00 O 830 8.00 N 776 7.00 C 3252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.02 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: 1.88 Conformation dependent library (CDL) restraints added in 900.4 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.604A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 123 removed outlier: 8.933A pdb=" N ILE A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 139 through 172 removed outlier: 4.262A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.298A pdb=" N TYR A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 225 removed outlier: 4.307A pdb=" N LEU A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.610A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.642A pdb=" N TRP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 4.231A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.919A pdb=" N LYS A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.972A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.958A pdb=" N ALA A 365 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.674A pdb=" N GLU A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 413 removed outlier: 3.655A pdb=" N SER A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.568A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 452 through 475 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.888A pdb=" N TYR A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 526 through 547 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 639 through 663 Processing helix chain 'B' and resid 29 through 53 removed outlier: 3.855A pdb=" N GLY B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.06 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: 726 1.31 - 1.44: 1394 1.44 - 1.57: 2833 1.57 - 1.70: 0 1.70 - 1.83: 67 Bond restraints: 5020 Sorted by residual: bond pdb=" C15 1YI A 701 " pdb=" O2 1YI A 701 " ideal model delta sigma weight residual 1.495 1.386 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C12 1YI A 701 " pdb=" O2 1YI A 701 " ideal model delta sigma weight residual 1.468 1.401 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C GLN B 22 " pdb=" N GLY B 23 " ideal model delta sigma weight residual 1.331 1.352 -0.021 6.60e-03 2.30e+04 1.04e+01 bond pdb=" C13 1YI A 701 " pdb=" O4 1YI A 701 " ideal model delta sigma weight residual 1.461 1.397 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CA GLY B 23 " pdb=" C GLY B 23 " ideal model delta sigma weight residual 1.517 1.496 0.022 7.00e-03 2.04e+04 9.70e+00 ... (remaining 5015 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.59: 84 104.59 - 112.04: 2467 112.04 - 119.48: 1811 119.48 - 126.93: 2407 126.93 - 134.37: 70 Bond angle restraints: 6839 Sorted by residual: angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 112.47 120.07 -7.60 2.06e+00 2.36e-01 1.36e+01 angle pdb=" C ILE A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 angle pdb=" N GLY A 95 " pdb=" CA GLY A 95 " pdb=" C GLY A 95 " ideal model delta sigma weight residual 113.18 119.64 -6.46 2.37e+00 1.78e-01 7.44e+00 angle pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 120.42 116.62 3.80 1.42e+00 4.96e-01 7.16e+00 angle pdb=" C LEU A 108 " pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 120.46 116.83 3.63 1.37e+00 5.33e-01 7.01e+00 ... (remaining 6834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.52: 2810 27.52 - 55.03: 82 55.03 - 82.55: 7 82.55 - 110.06: 0 110.06 - 137.58: 1 Dihedral angle restraints: 2900 sinusoidal: 1077 harmonic: 1823 Sorted by residual: dihedral pdb=" CA PHE A 251 " pdb=" C PHE A 251 " pdb=" N GLN A 252 " pdb=" CA GLN A 252 " ideal model delta harmonic sigma weight residual 180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL A 359 " pdb=" C VAL A 359 " pdb=" N GLY A 360 " pdb=" CA GLY A 360 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C31 1YI A 701 " pdb=" C29 1YI A 701 " pdb=" C30 1YI A 701 " pdb=" C33 1YI A 701 " ideal model delta sinusoidal sigma weight residual 89.77 -47.81 137.58 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 2897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 534 0.042 - 0.084: 219 0.084 - 0.126: 51 0.126 - 0.168: 8 0.168 - 0.210: 5 Chirality restraints: 817 Sorted by residual: chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 109 " pdb=" CA VAL A 109 " pdb=" CG1 VAL A 109 " pdb=" CG2 VAL A 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 814 not shown) Planarity restraints: 823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 513 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 514 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 279 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.43e+00 pdb=" C PHE A 279 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE A 279 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 280 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 240 " -0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 241 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.037 5.00e-02 4.00e+02 ... (remaining 820 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 651 2.75 - 3.29: 5426 3.29 - 3.83: 8511 3.83 - 4.36: 9866 4.36 - 4.90: 17071 Nonbonded interactions: 41525 Sorted by model distance: nonbonded pdb=" OE1 GLN A 142 " pdb=" NZ LYS A 412 " model vdw 2.213 2.520 nonbonded pdb=" NE2 GLN A 142 " pdb=" OD1 ASP A 408 " model vdw 2.214 2.520 nonbonded pdb=" NH1 ARG A 499 " pdb=" OE1 GLU A 503 " model vdw 2.274 2.520 nonbonded pdb=" OH TYR A 462 " pdb=" NH1 ARG A 499 " model vdw 2.274 2.520 nonbonded pdb=" OG SER A 77 " pdb=" OG SER A 396 " model vdw 2.283 2.440 ... (remaining 41520 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: 1.250 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: 4.840 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 5020 Z= 0.455 Angle : 0.942 8.566 6839 Z= 0.493 Chirality : 0.048 0.210 817 Planarity : 0.008 0.070 823 Dihedral : 12.393 137.579 1725 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 1.75 % Allowed : 3.51 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.33), residues: 630 helix: 0.58 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.55 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 477 HIS 0.004 0.002 HIS A 83 PHE 0.030 0.003 PHE A 168 TYR 0.017 0.002 TYR A 506 ARG 0.004 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.5944 (mtt90) cc_final: 0.5216 (mtp-110) REVERT: A 163 PHE cc_start: 0.6054 (t80) cc_final: 0.5469 (t80) REVERT: A 202 TYR cc_start: 0.7006 (m-80) cc_final: 0.6636 (m-10) REVERT: A 204 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.5630 (t0) REVERT: A 330 MET cc_start: 0.7763 (mmt) cc_final: 0.7201 (mmt) REVERT: A 374 MET cc_start: 0.7297 (mtp) cc_final: 0.6933 (mtp) REVERT: A 382 MET cc_start: 0.5794 (tpt) cc_final: 0.5395 (mmm) REVERT: A 416 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6863 (mtm180) REVERT: A 445 GLN cc_start: 0.6498 (tm-30) cc_final: 0.5656 (tt0) REVERT: A 512 MET cc_start: 0.5364 (tpt) cc_final: 0.4621 (tpp) REVERT: A 555 HIS cc_start: 0.8369 (m170) cc_final: 0.7931 (m-70) REVERT: A 630 MET cc_start: 0.6179 (mmm) cc_final: 0.5563 (mpp) REVERT: B 31 MET cc_start: 0.6951 (ttm) cc_final: 0.6133 (tpt) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.2200 time to fit residues: 27.4221 Evaluate side-chains 72 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 520 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5020 Z= 0.250 Angle : 0.676 12.413 6839 Z= 0.342 Chirality : 0.045 0.190 817 Planarity : 0.006 0.054 823 Dihedral : 7.022 110.002 702 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.76 % Favored : 95.08 % Rotamer: Outliers : 0.97 % Allowed : 9.16 % Favored : 89.86 % 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: 0.70 (0.34), residues: 630 helix: 1.12 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.002 0.001 HIS A 660 PHE 0.023 0.002 PHE A 168 TYR 0.012 0.002 TYR A 191 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7599 (m-10) cc_final: 0.7306 (m-10) REVERT: A 63 ARG cc_start: 0.6093 (mtt90) cc_final: 0.5388 (mtp-110) REVERT: A 163 PHE cc_start: 0.5938 (t80) cc_final: 0.5486 (t80) REVERT: A 353 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7917 (ptmt) REVERT: A 374 MET cc_start: 0.7181 (mtp) cc_final: 0.6932 (mtp) REVERT: A 416 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7057 (mtm110) REVERT: A 445 GLN cc_start: 0.6454 (tm-30) cc_final: 0.5501 (tt0) REVERT: A 555 HIS cc_start: 0.8388 (m170) cc_final: 0.8159 (m90) REVERT: A 630 MET cc_start: 0.6297 (mmm) cc_final: 0.5602 (mpp) REVERT: B 31 MET cc_start: 0.7096 (ttm) cc_final: 0.6209 (tpt) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.1856 time to fit residues: 18.1686 Evaluate side-chains 64 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 355 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7032 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5020 Z= 0.247 Angle : 0.653 9.705 6839 Z= 0.329 Chirality : 0.044 0.173 817 Planarity : 0.005 0.050 823 Dihedral : 6.443 101.009 694 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.95 % Allowed : 12.28 % Favored : 85.77 % 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: 0.74 (0.34), residues: 630 helix: 1.18 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -1.37 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 83 PHE 0.023 0.002 PHE A 168 TYR 0.010 0.002 TYR A 191 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 48 PHE cc_start: 0.7662 (m-10) cc_final: 0.7332 (m-10) REVERT: A 63 ARG cc_start: 0.6094 (mtt90) cc_final: 0.5070 (mtp-110) REVERT: A 163 PHE cc_start: 0.5940 (t80) cc_final: 0.5654 (t80) REVERT: A 382 MET cc_start: 0.5381 (mmm) cc_final: 0.5165 (mmm) REVERT: A 414 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6379 (mtm180) REVERT: A 416 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7092 (mtm110) REVERT: A 445 GLN cc_start: 0.6283 (tm-30) cc_final: 0.5347 (tt0) REVERT: A 555 HIS cc_start: 0.8441 (m170) cc_final: 0.8069 (m-70) REVERT: A 630 MET cc_start: 0.6418 (mmm) cc_final: 0.5672 (mpp) REVERT: B 31 MET cc_start: 0.7096 (ttm) cc_final: 0.6798 (ttm) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.1792 time to fit residues: 16.6890 Evaluate side-chains 64 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 355 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5020 Z= 0.232 Angle : 0.621 10.466 6839 Z= 0.315 Chirality : 0.043 0.163 817 Planarity : 0.005 0.049 823 Dihedral : 6.308 97.751 691 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.92 % Allowed : 12.48 % Favored : 84.60 % 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: 0.79 (0.34), residues: 630 helix: 1.23 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 641 HIS 0.003 0.001 HIS A 83 PHE 0.023 0.002 PHE A 168 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7322 (mm) cc_final: 0.6736 (pt) REVERT: A 48 PHE cc_start: 0.7699 (m-10) cc_final: 0.7349 (m-10) REVERT: A 63 ARG cc_start: 0.6124 (mtt90) cc_final: 0.5090 (mtp-110) REVERT: A 163 PHE cc_start: 0.5888 (t80) cc_final: 0.5544 (t80) REVERT: A 382 MET cc_start: 0.5434 (mmm) cc_final: 0.5168 (mmm) REVERT: A 416 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7081 (mtm110) REVERT: A 445 GLN cc_start: 0.6142 (tm-30) cc_final: 0.5241 (tt0) REVERT: A 555 HIS cc_start: 0.8510 (m170) cc_final: 0.8177 (m-70) REVERT: A 630 MET cc_start: 0.6392 (mmm) cc_final: 0.5593 (mpp) REVERT: B 31 MET cc_start: 0.7112 (ttm) cc_final: 0.6838 (ttm) outliers start: 15 outliers final: 11 residues processed: 76 average time/residue: 0.1715 time to fit residues: 16.9558 Evaluate side-chains 69 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5020 Z= 0.234 Angle : 0.619 10.181 6839 Z= 0.313 Chirality : 0.043 0.161 817 Planarity : 0.005 0.048 823 Dihedral : 6.234 94.858 691 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.51 % Allowed : 13.65 % Favored : 82.85 % 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: 0.80 (0.34), residues: 630 helix: 1.24 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 641 HIS 0.003 0.001 HIS A 83 PHE 0.023 0.002 PHE A 168 TYR 0.009 0.001 TYR A 153 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6114 (mtt90) cc_final: 0.5020 (mtp-110) REVERT: A 163 PHE cc_start: 0.5885 (t80) cc_final: 0.5529 (t80) REVERT: A 171 LEU cc_start: 0.6502 (tp) cc_final: 0.6284 (tt) REVERT: A 416 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7121 (mtm180) REVERT: A 445 GLN cc_start: 0.5937 (tm-30) cc_final: 0.5068 (tt0) REVERT: A 630 MET cc_start: 0.6469 (mmm) cc_final: 0.5635 (mpp) REVERT: B 31 MET cc_start: 0.7068 (ttm) cc_final: 0.6780 (ttm) outliers start: 18 outliers final: 13 residues processed: 92 average time/residue: 0.1542 time to fit residues: 18.7797 Evaluate side-chains 77 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 overall best weight: 0.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5020 Z= 0.167 Angle : 0.601 10.160 6839 Z= 0.299 Chirality : 0.041 0.176 817 Planarity : 0.005 0.048 823 Dihedral : 5.916 84.686 691 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.29 % Allowed : 14.62 % Favored : 81.09 % 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: 0.96 (0.34), residues: 630 helix: 1.31 (0.25), residues: 467 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 68 HIS 0.002 0.001 HIS A 83 PHE 0.020 0.001 PHE A 168 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7236 (mm) cc_final: 0.6720 (pt) REVERT: A 63 ARG cc_start: 0.6110 (mtt90) cc_final: 0.5014 (mtp-110) REVERT: A 163 PHE cc_start: 0.5804 (t80) cc_final: 0.5494 (t80) REVERT: A 416 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7401 (mmt90) REVERT: A 630 MET cc_start: 0.6419 (mmm) cc_final: 0.5619 (mpp) REVERT: B 31 MET cc_start: 0.7114 (ttm) cc_final: 0.6814 (ttm) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 0.1646 time to fit residues: 17.5602 Evaluate side-chains 74 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.0020 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5020 Z= 0.183 Angle : 0.614 10.525 6839 Z= 0.302 Chirality : 0.042 0.176 817 Planarity : 0.005 0.047 823 Dihedral : 5.723 78.673 691 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.48 % Allowed : 13.84 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.34), residues: 630 helix: 1.37 (0.25), residues: 465 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 68 HIS 0.003 0.001 HIS A 83 PHE 0.021 0.001 PHE A 168 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7301 (mm) cc_final: 0.6777 (pt) REVERT: A 63 ARG cc_start: 0.6131 (mtt90) cc_final: 0.5070 (mtp-110) REVERT: A 163 PHE cc_start: 0.5823 (t80) cc_final: 0.5546 (t80) REVERT: A 407 MET cc_start: 0.8192 (mmm) cc_final: 0.7967 (mmm) REVERT: A 630 MET cc_start: 0.6429 (mmm) cc_final: 0.5618 (mpp) REVERT: B 31 MET cc_start: 0.7114 (ttm) cc_final: 0.6797 (ttm) outliers start: 23 outliers final: 20 residues processed: 81 average time/residue: 0.1635 time to fit residues: 17.5752 Evaluate side-chains 77 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5020 Z= 0.185 Angle : 0.613 11.695 6839 Z= 0.302 Chirality : 0.041 0.171 817 Planarity : 0.005 0.047 823 Dihedral : 5.674 76.031 691 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.29 % Allowed : 14.04 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.34), residues: 630 helix: 1.44 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 641 HIS 0.004 0.001 HIS A 83 PHE 0.021 0.001 PHE A 168 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7336 (mm) cc_final: 0.6815 (pt) REVERT: A 63 ARG cc_start: 0.6152 (mtt90) cc_final: 0.5042 (mtp-110) REVERT: A 163 PHE cc_start: 0.5834 (t80) cc_final: 0.5569 (t80) REVERT: A 407 MET cc_start: 0.8235 (mmm) cc_final: 0.7981 (mmm) REVERT: A 630 MET cc_start: 0.6472 (mmm) cc_final: 0.5655 (mpp) REVERT: B 31 MET cc_start: 0.7079 (ttm) cc_final: 0.6748 (ttm) outliers start: 22 outliers final: 19 residues processed: 76 average time/residue: 0.1758 time to fit residues: 17.3522 Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5020 Z= 0.223 Angle : 0.642 13.050 6839 Z= 0.314 Chirality : 0.043 0.173 817 Planarity : 0.005 0.047 823 Dihedral : 5.754 76.932 691 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.48 % Allowed : 13.65 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.34), residues: 630 helix: 1.36 (0.25), residues: 469 sheet: None (None), residues: 0 loop : -1.43 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 641 HIS 0.004 0.001 HIS A 83 PHE 0.024 0.002 PHE A 168 TYR 0.009 0.001 TYR A 153 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7332 (mm) cc_final: 0.6793 (pt) REVERT: A 63 ARG cc_start: 0.6160 (mtt90) cc_final: 0.5023 (mtp-110) REVERT: A 407 MET cc_start: 0.8262 (mmm) cc_final: 0.7999 (mmm) REVERT: A 477 TRP cc_start: 0.6828 (t-100) cc_final: 0.6287 (t-100) REVERT: A 630 MET cc_start: 0.6545 (mmm) cc_final: 0.5683 (mpp) REVERT: B 31 MET cc_start: 0.7040 (ttm) cc_final: 0.6717 (ttm) outliers start: 23 outliers final: 20 residues processed: 85 average time/residue: 0.1614 time to fit residues: 18.2462 Evaluate side-chains 82 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 7 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5020 Z= 0.195 Angle : 0.633 12.473 6839 Z= 0.310 Chirality : 0.042 0.169 817 Planarity : 0.005 0.047 823 Dihedral : 5.695 74.087 691 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.29 % Allowed : 14.81 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.34), residues: 630 helix: 1.26 (0.24), residues: 474 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 641 HIS 0.003 0.001 HIS A 83 PHE 0.021 0.002 PHE A 168 TYR 0.009 0.001 TYR A 153 ARG 0.002 0.000 ARG A 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7328 (mm) cc_final: 0.6791 (pt) REVERT: A 63 ARG cc_start: 0.6112 (mtt90) cc_final: 0.4987 (mtp-110) REVERT: A 407 MET cc_start: 0.8279 (mmm) cc_final: 0.8011 (mmm) REVERT: A 477 TRP cc_start: 0.6736 (t-100) cc_final: 0.6014 (t-100) REVERT: A 630 MET cc_start: 0.6565 (mmm) cc_final: 0.5709 (mpp) REVERT: B 31 MET cc_start: 0.7054 (ttm) cc_final: 0.6728 (ttm) outliers start: 22 outliers final: 21 residues processed: 77 average time/residue: 0.1640 time to fit residues: 16.7688 Evaluate side-chains 80 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 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 = 0.4080 r_free = 0.4080 target = 0.186217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167442 restraints weight = 5538.226| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.28 r_work: 0.3718 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5020 Z= 0.219 Angle : 0.642 13.611 6839 Z= 0.315 Chirality : 0.043 0.173 817 Planarity : 0.005 0.047 823 Dihedral : 5.706 72.885 691 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.09 % Allowed : 15.01 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.34), residues: 630 helix: 1.30 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 641 HIS 0.004 0.001 HIS A 83 PHE 0.020 0.002 PHE A 163 TYR 0.010 0.001 TYR A 153 ARG 0.002 0.000 ARG A 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.10 seconds wall clock time: 26 minutes 27.36 seconds (1587.36 seconds total)