Starting phenix.real_space_refine on Fri Aug 2 17:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/08_2024/8wx5_37901.cif" } resolution = 3.91 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= 0.001 sd= 0.052 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 22 5.16 5 C 2552 2.51 5 N 619 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3857 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3741 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 22, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 2.91, per 1000 atoms: 0.75 Number of scatterers: 3857 At special positions: 0 Unit cell: (80.51, 77.19, 73.87, 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 22 16.00 O 664 8.00 N 619 7.00 C 2552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 152 " distance=2.03 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: 1.62 Conformation dependent library (CDL) restraints added in 693.0 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 57 removed outlier: 3.927A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.539A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 97 Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 125 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 146 through 185 removed outlier: 3.514A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.443A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 4.049A pdb=" N ASP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 Processing helix chain 'A' and resid 221 through 245 Proline residue: A 229 - end of helix removed outlier: 4.111A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 310 through 349 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 354 through 358 removed outlier: 4.283A pdb=" N ILE A 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 394 Proline residue: A 382 - end of helix Proline residue: A 390 - end of helix removed outlier: 3.897A pdb=" N ARG A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 479 removed outlier: 4.550A pdb=" N GLN A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 512 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 556 removed outlier: 4.067A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.715A pdb=" N GLN A 437 " --> pdb=" O TYR A 444 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 930 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: 1.06 Time building geometry restraints manager: 1.76 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: 588 1.31 - 1.43: 1104 1.43 - 1.56: 2230 1.56 - 1.69: 0 1.69 - 1.82: 33 Bond restraints: 3955 Sorted by residual: bond pdb=" C SER B 8 " pdb=" O SER B 8 " ideal model delta sigma weight residual 1.236 1.307 -0.070 1.24e-02 6.50e+03 3.21e+01 bond pdb=" C LEU B 7 " pdb=" O LEU B 7 " ideal model delta sigma weight residual 1.236 1.294 -0.058 1.19e-02 7.06e+03 2.34e+01 bond pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.69e-02 3.50e+03 2.11e+01 bond pdb=" C TYR B 6 " pdb=" O TYR B 6 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.26e-02 6.30e+03 1.84e+01 bond pdb=" C GLY B 9 " pdb=" O GLY B 9 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.35e-02 5.49e+03 1.72e+01 ... (remaining 3950 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.25: 132 107.25 - 114.04: 2237 114.04 - 120.83: 1887 120.83 - 127.62: 1091 127.62 - 134.42: 37 Bond angle restraints: 5384 Sorted by residual: angle pdb=" N GLU B 4 " pdb=" CA GLU B 4 " pdb=" C GLU B 4 " ideal model delta sigma weight residual 112.34 102.39 9.95 1.30e+00 5.92e-01 5.86e+01 angle pdb=" N LEU B 10 " pdb=" CA LEU B 10 " pdb=" C LEU B 10 " ideal model delta sigma weight residual 111.37 100.45 10.92 1.64e+00 3.72e-01 4.43e+01 angle pdb=" N TRP B 13 " pdb=" CA TRP B 13 " pdb=" C TRP B 13 " ideal model delta sigma weight residual 111.37 102.04 9.33 1.65e+00 3.67e-01 3.20e+01 angle pdb=" N SER B 8 " pdb=" CA SER B 8 " pdb=" C SER B 8 " ideal model delta sigma weight residual 111.75 104.52 7.23 1.28e+00 6.10e-01 3.19e+01 angle pdb=" N TYR B 12 " pdb=" CA TYR B 12 " pdb=" C TYR B 12 " ideal model delta sigma weight residual 111.36 117.06 -5.70 1.09e+00 8.42e-01 2.73e+01 ... (remaining 5379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2037 17.98 - 35.95: 206 35.95 - 53.93: 43 53.93 - 71.91: 3 71.91 - 89.89: 2 Dihedral angle restraints: 2291 sinusoidal: 849 harmonic: 1442 Sorted by residual: dihedral pdb=" N SER B 8 " pdb=" C SER B 8 " pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta harmonic sigma weight residual 122.80 112.32 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" N LEU B 10 " pdb=" C LEU B 10 " pdb=" CA LEU B 10 " pdb=" CB LEU B 10 " ideal model delta harmonic sigma weight residual 122.80 112.37 10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C TRP B 13 " pdb=" N TRP B 13 " pdb=" CA TRP B 13 " pdb=" CB TRP B 13 " ideal model delta harmonic sigma weight residual -122.60 -113.16 -9.44 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 2288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 564 0.064 - 0.128: 57 0.128 - 0.192: 3 0.192 - 0.256: 1 0.256 - 0.319: 3 Chirality restraints: 628 Sorted by residual: chirality pdb=" CA TRP B 13 " pdb=" N TRP B 13 " pdb=" C TRP B 13 " pdb=" CB TRP B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA TYR B 12 " pdb=" N TYR B 12 " pdb=" C TYR B 12 " pdb=" CB TYR B 12 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LEU B 10 " pdb=" N LEU B 10 " pdb=" C LEU B 10 " pdb=" CB LEU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 625 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 9 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C GLY B 9 " -0.071 2.00e-02 2.50e+03 pdb=" O GLY B 9 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 10 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 10 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C LEU B 10 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 10 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 11 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 229 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.029 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 215 2.73 - 3.27: 4249 3.27 - 3.81: 6741 3.81 - 4.36: 7416 4.36 - 4.90: 12796 Nonbonded interactions: 31417 Sorted by model distance: nonbonded pdb=" O LEU A 349 " pdb=" NE2 GLN A 437 " model vdw 2.184 3.120 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 341 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 355 " pdb=" O THR A 358 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.259 3.040 nonbonded pdb=" O LEU A 380 " pdb=" N LYS A 384 " model vdw 2.280 3.120 ... (remaining 31412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.004 0.078 3955 Z= 0.255 Angle : 0.867 10.916 5384 Z= 0.555 Chirality : 0.044 0.319 628 Planarity : 0.005 0.051 664 Dihedral : 14.579 89.886 1363 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.63 % Favored : 92.97 % Rotamer: Outliers : 0.50 % Allowed : 6.98 % Favored : 92.52 % 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: -1.72 (0.34), residues: 498 helix: -0.26 (0.24), residues: 389 sheet: -4.91 (0.87), residues: 10 loop : -4.00 (0.45), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 13 HIS 0.002 0.000 HIS A 362 PHE 0.012 0.001 PHE A 67 TYR 0.022 0.002 TYR B 12 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9316 (mt) cc_final: 0.9044 (mt) REVERT: A 63 ASN cc_start: 0.7813 (m110) cc_final: 0.7512 (t0) REVERT: A 259 ASP cc_start: 0.9094 (m-30) cc_final: 0.8872 (m-30) REVERT: A 310 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 409 MET cc_start: 0.9073 (mtt) cc_final: 0.8799 (mtt) REVERT: A 453 TRP cc_start: 0.7998 (m100) cc_final: 0.7208 (m100) REVERT: A 465 GLU cc_start: 0.9358 (tp30) cc_final: 0.9097 (tp30) REVERT: A 470 ILE cc_start: 0.8834 (mm) cc_final: 0.8583 (mm) REVERT: A 474 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7222 (mt-10) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.1410 time to fit residues: 27.9735 Evaluate side-chains 129 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 356 ASN A 441 ASN A 454 GLN B 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3955 Z= 0.195 Angle : 0.656 7.811 5384 Z= 0.335 Chirality : 0.041 0.161 628 Planarity : 0.005 0.052 664 Dihedral : 4.704 16.291 538 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.99 % Allowed : 16.46 % Favored : 79.55 % 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: -0.10 (0.38), residues: 498 helix: 0.81 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -3.29 (0.50), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 13 HIS 0.003 0.001 HIS A 348 PHE 0.018 0.001 PHE A 194 TYR 0.034 0.002 TYR B 12 ARG 0.008 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9539 (mt) cc_final: 0.9121 (mp) REVERT: A 120 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8397 (t80) REVERT: A 240 PHE cc_start: 0.9079 (t80) cc_final: 0.8874 (t80) REVERT: A 259 ASP cc_start: 0.9111 (m-30) cc_final: 0.8908 (m-30) REVERT: A 409 MET cc_start: 0.9108 (mtt) cc_final: 0.8708 (mtt) REVERT: A 423 GLU cc_start: 0.8506 (tp30) cc_final: 0.8166 (tp30) REVERT: A 426 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8404 (ttp80) REVERT: A 453 TRP cc_start: 0.8103 (m100) cc_final: 0.7436 (m100) REVERT: A 465 GLU cc_start: 0.9389 (tp30) cc_final: 0.8958 (tp30) REVERT: A 470 ILE cc_start: 0.8751 (mm) cc_final: 0.8476 (mm) REVERT: A 474 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 501 PHE cc_start: 0.8593 (m-80) cc_final: 0.7569 (t80) REVERT: A 543 GLN cc_start: 0.9507 (tp40) cc_final: 0.8997 (tp-100) REVERT: B 13 TRP cc_start: 0.5785 (OUTLIER) cc_final: 0.4626 (t-100) outliers start: 16 outliers final: 8 residues processed: 147 average time/residue: 0.1241 time to fit residues: 23.7178 Evaluate side-chains 136 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3955 Z= 0.195 Angle : 0.658 8.272 5384 Z= 0.335 Chirality : 0.042 0.152 628 Planarity : 0.005 0.059 664 Dihedral : 4.650 16.395 537 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.24 % Allowed : 20.70 % Favored : 75.06 % 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: 0.38 (0.38), residues: 498 helix: 1.03 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -2.83 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.001 0.001 HIS A 348 PHE 0.011 0.001 PHE A 195 TYR 0.027 0.002 TYR B 12 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8947 (m-10) cc_final: 0.8467 (m-10) REVERT: A 120 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7978 (t80) REVERT: A 259 ASP cc_start: 0.9140 (m-30) cc_final: 0.8935 (m-30) REVERT: A 423 GLU cc_start: 0.8503 (tp30) cc_final: 0.8165 (tp30) REVERT: A 453 TRP cc_start: 0.8084 (m100) cc_final: 0.7395 (m100) REVERT: A 465 GLU cc_start: 0.9316 (tp30) cc_final: 0.8948 (tp30) REVERT: A 470 ILE cc_start: 0.8677 (mm) cc_final: 0.8382 (mm) REVERT: A 474 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 501 PHE cc_start: 0.8608 (m-80) cc_final: 0.7619 (t80) outliers start: 17 outliers final: 10 residues processed: 135 average time/residue: 0.1187 time to fit residues: 21.2502 Evaluate side-chains 135 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3955 Z= 0.206 Angle : 0.642 9.200 5384 Z= 0.328 Chirality : 0.041 0.132 628 Planarity : 0.005 0.052 664 Dihedral : 4.559 16.460 537 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.74 % Allowed : 26.18 % Favored : 69.08 % 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: 0.60 (0.39), residues: 498 helix: 1.16 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -2.67 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 195 TYR 0.025 0.002 TYR B 12 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.7275 (m100) cc_final: 0.6905 (m100) REVERT: A 203 ASN cc_start: 0.8670 (m-40) cc_final: 0.8326 (m-40) REVERT: A 259 ASP cc_start: 0.9158 (m-30) cc_final: 0.8948 (m-30) REVERT: A 316 LYS cc_start: 0.8860 (tttt) cc_final: 0.8639 (ttmt) REVERT: A 426 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8565 (ttp80) REVERT: A 453 TRP cc_start: 0.8107 (m100) cc_final: 0.7427 (m100) REVERT: A 465 GLU cc_start: 0.9304 (tp30) cc_final: 0.8984 (tp30) REVERT: A 470 ILE cc_start: 0.8680 (mm) cc_final: 0.8368 (mm) REVERT: A 474 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 501 PHE cc_start: 0.8623 (m-80) cc_final: 0.7664 (t80) REVERT: B 13 TRP cc_start: 0.5790 (OUTLIER) cc_final: 0.5194 (m100) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.1225 time to fit residues: 22.1287 Evaluate side-chains 137 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3955 Z= 0.224 Angle : 0.661 9.524 5384 Z= 0.334 Chirality : 0.041 0.138 628 Planarity : 0.005 0.049 664 Dihedral : 4.525 17.111 537 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.99 % Allowed : 29.18 % Favored : 66.83 % 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: 0.61 (0.39), residues: 498 helix: 1.15 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -2.57 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 67 TYR 0.023 0.002 TYR A 331 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.7299 (m100) cc_final: 0.6958 (m100) REVERT: A 203 ASN cc_start: 0.8673 (m-40) cc_final: 0.8315 (m-40) REVERT: A 259 ASP cc_start: 0.9171 (m-30) cc_final: 0.8964 (m-30) REVERT: A 310 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 423 GLU cc_start: 0.8553 (tp30) cc_final: 0.8254 (tp30) REVERT: A 426 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8572 (ttp80) REVERT: A 453 TRP cc_start: 0.8177 (m100) cc_final: 0.7495 (m100) REVERT: A 465 GLU cc_start: 0.9288 (tp30) cc_final: 0.9007 (tp30) REVERT: A 470 ILE cc_start: 0.8662 (mm) cc_final: 0.8328 (mm) REVERT: A 474 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 501 PHE cc_start: 0.8650 (m-80) cc_final: 0.7709 (t80) REVERT: B 13 TRP cc_start: 0.5754 (OUTLIER) cc_final: 0.5169 (m100) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.1191 time to fit residues: 20.5646 Evaluate side-chains 134 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3955 Z= 0.205 Angle : 0.663 10.481 5384 Z= 0.335 Chirality : 0.041 0.134 628 Planarity : 0.005 0.046 664 Dihedral : 4.512 17.085 537 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.99 % Allowed : 29.43 % Favored : 66.58 % 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 (0.39), residues: 498 helix: 1.20 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -2.46 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 411 TYR 0.023 0.002 TYR B 12 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.7344 (m100) cc_final: 0.7129 (m100) REVERT: A 259 ASP cc_start: 0.9202 (m-30) cc_final: 0.8990 (m-30) REVERT: A 423 GLU cc_start: 0.8513 (tp30) cc_final: 0.8238 (tp30) REVERT: A 426 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8559 (ttp80) REVERT: A 453 TRP cc_start: 0.8159 (m100) cc_final: 0.7494 (m100) REVERT: A 465 GLU cc_start: 0.9264 (tp30) cc_final: 0.8998 (tp30) REVERT: A 470 ILE cc_start: 0.8617 (mm) cc_final: 0.8343 (mm) REVERT: A 474 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 501 PHE cc_start: 0.8648 (m-80) cc_final: 0.7719 (t80) REVERT: B 13 TRP cc_start: 0.5688 (OUTLIER) cc_final: 0.5200 (m100) outliers start: 16 outliers final: 11 residues processed: 133 average time/residue: 0.1228 time to fit residues: 21.0763 Evaluate side-chains 133 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.198 Angle : 0.679 11.418 5384 Z= 0.338 Chirality : 0.040 0.131 628 Planarity : 0.005 0.044 664 Dihedral : 4.512 16.697 537 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.99 % Allowed : 30.17 % Favored : 65.84 % 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: 0.76 (0.39), residues: 498 helix: 1.23 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -2.39 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 411 TYR 0.021 0.002 TYR B 12 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TRP cc_start: 0.7317 (m100) cc_final: 0.7109 (m100) REVERT: A 259 ASP cc_start: 0.9204 (m-30) cc_final: 0.9001 (m-30) REVERT: A 426 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8536 (ttp80) REVERT: A 453 TRP cc_start: 0.8148 (m100) cc_final: 0.7491 (m100) REVERT: A 474 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 501 PHE cc_start: 0.8643 (m-80) cc_final: 0.7754 (t80) REVERT: B 13 TRP cc_start: 0.5666 (OUTLIER) cc_final: 0.5277 (m100) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.1165 time to fit residues: 21.0026 Evaluate side-chains 136 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3955 Z= 0.228 Angle : 0.695 11.507 5384 Z= 0.351 Chirality : 0.041 0.156 628 Planarity : 0.005 0.043 664 Dihedral : 4.486 17.691 537 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.99 % Allowed : 31.42 % Favored : 64.59 % 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: 0.68 (0.39), residues: 498 helix: 1.18 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.49 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 94 HIS 0.002 0.000 HIS A 348 PHE 0.012 0.001 PHE A 411 TYR 0.019 0.002 TYR B 12 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8523 (m-30) cc_final: 0.7230 (t0) REVERT: A 316 LYS cc_start: 0.8899 (tttt) cc_final: 0.8672 (ttmt) REVERT: A 423 GLU cc_start: 0.8472 (tp30) cc_final: 0.8235 (tp30) REVERT: A 426 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8561 (ttp80) REVERT: A 453 TRP cc_start: 0.8238 (m100) cc_final: 0.7557 (m100) REVERT: A 474 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 501 PHE cc_start: 0.8657 (m-80) cc_final: 0.7772 (t80) REVERT: B 13 TRP cc_start: 0.5758 (OUTLIER) cc_final: 0.5284 (m100) outliers start: 16 outliers final: 14 residues processed: 126 average time/residue: 0.1134 time to fit residues: 18.7751 Evaluate side-chains 132 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3955 Z= 0.239 Angle : 0.726 12.400 5384 Z= 0.362 Chirality : 0.042 0.150 628 Planarity : 0.005 0.043 664 Dihedral : 4.519 18.077 537 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.74 % Allowed : 32.67 % Favored : 63.59 % 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: 0.66 (0.39), residues: 498 helix: 1.17 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.54 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.002 0.000 HIS A 348 PHE 0.010 0.001 PHE A 411 TYR 0.019 0.002 TYR B 12 ARG 0.001 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8448 (tp30) cc_final: 0.8212 (tp30) REVERT: A 426 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8559 (ttp80) REVERT: A 453 TRP cc_start: 0.8266 (m100) cc_final: 0.7424 (m100) REVERT: A 474 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 501 PHE cc_start: 0.8699 (m-80) cc_final: 0.7797 (t80) REVERT: B 13 TRP cc_start: 0.5759 (OUTLIER) cc_final: 0.5147 (m100) outliers start: 15 outliers final: 13 residues processed: 131 average time/residue: 0.1200 time to fit residues: 20.5649 Evaluate side-chains 139 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3955 Z= 0.226 Angle : 0.727 12.084 5384 Z= 0.364 Chirality : 0.042 0.160 628 Planarity : 0.005 0.043 664 Dihedral : 4.495 17.692 537 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.24 % Allowed : 33.17 % Favored : 63.59 % 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: 0.67 (0.39), residues: 498 helix: 1.18 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.50 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.013 0.001 PHE A 411 TYR 0.019 0.001 TYR B 12 ARG 0.001 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LYS cc_start: 0.8885 (tttt) cc_final: 0.8668 (ttmt) REVERT: A 423 GLU cc_start: 0.8403 (tp30) cc_final: 0.8171 (tp30) REVERT: A 426 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8560 (ttp80) REVERT: A 453 TRP cc_start: 0.8250 (m100) cc_final: 0.7415 (m100) REVERT: A 474 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 501 PHE cc_start: 0.8579 (m-80) cc_final: 0.7732 (t80) REVERT: B 13 TRP cc_start: 0.5766 (OUTLIER) cc_final: 0.5211 (m100) outliers start: 13 outliers final: 12 residues processed: 135 average time/residue: 0.1257 time to fit residues: 22.1142 Evaluate side-chains 140 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 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 = 0.3756 r_free = 0.3756 target = 0.144800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120494 restraints weight = 7516.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124196 restraints weight = 4304.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126815 restraints weight = 2907.995| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3955 Z= 0.225 Angle : 0.729 12.079 5384 Z= 0.363 Chirality : 0.041 0.152 628 Planarity : 0.005 0.043 664 Dihedral : 4.496 17.482 537 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.24 % Allowed : 33.17 % Favored : 63.59 % 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: 0.73 (0.39), residues: 498 helix: 1.19 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.38 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.015 0.001 PHE A 411 TYR 0.018 0.002 TYR B 12 ARG 0.001 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.29 seconds wall clock time: 23 minutes 7.30 seconds (1387.30 seconds total)