Starting phenix.real_space_refine on Sun Mar 10 17:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/03_2024/7wsm_32760_updated.pdb" } resolution = 3.25 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= -0.003 sd= 0.090 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 14 5.16 5 C 2359 2.51 5 N 582 2.21 5 O 622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3577 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3514 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'5RH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.73 Number of scatterers: 3577 At special positions: 0 Unit cell: (86.6, 56.29, 83.3525, 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 14 16.00 O 622 8.00 N 582 7.00 C 2359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 57 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 626.7 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 Processing helix chain 'A' and resid 47 through 67 removed outlier: 4.433A pdb=" N LYS A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 53 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 63 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 65 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 74 through 98 removed outlier: 4.162A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 136 through 163 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 169 through 189 removed outlier: 3.795A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 222 removed outlier: 3.631A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Proline residue: A 212 - end of helix Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.613A pdb=" N ASP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 282 through 299 removed outlier: 4.604A pdb=" N GLN A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.661A pdb=" N SER A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 4.373A pdb=" N GLU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 372 Processing helix chain 'A' and resid 378 through 397 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 416 through 445 removed outlier: 5.858A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 467 removed outlier: 4.028A pdb=" N PHE A 450 " --> pdb=" O PRO A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 249 hydrogen bonds defined for protein. 576 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: 1.11 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 550 1.32 - 1.44: 969 1.44 - 1.56: 2116 1.56 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3660 Sorted by residual: bond pdb=" C TRP A 60 " pdb=" O TRP A 60 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.64e+00 bond pdb=" C TRP A 60 " pdb=" N LEU A 61 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.45e-02 4.76e+03 8.81e+00 bond pdb=" CA ALA A 364 " pdb=" CB ALA A 364 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.66e-02 3.63e+03 8.69e+00 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.58e+00 bond pdb=" N ILE A 479 " pdb=" CA ILE A 479 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.14e-02 7.69e+03 6.30e+00 ... (remaining 3655 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.57: 151 107.57 - 114.30: 2111 114.30 - 121.02: 1900 121.02 - 127.75: 789 127.75 - 134.47: 39 Bond angle restraints: 4990 Sorted by residual: angle pdb=" N LEU A 61 " pdb=" CA LEU A 61 " pdb=" C LEU A 61 " ideal model delta sigma weight residual 112.45 103.58 8.87 1.39e+00 5.18e-01 4.07e+01 angle pdb=" N PHE A 476 " pdb=" CA PHE A 476 " pdb=" C PHE A 476 " ideal model delta sigma weight residual 111.75 103.68 8.07 1.28e+00 6.10e-01 3.98e+01 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" C LEU A 366 " ideal model delta sigma weight residual 111.14 104.95 6.19 1.08e+00 8.57e-01 3.28e+01 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 113.27 106.78 6.49 1.33e+00 5.65e-01 2.38e+01 angle pdb=" C TRP A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 121.64 112.03 9.61 2.13e+00 2.20e-01 2.04e+01 ... (remaining 4985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 2156 35.97 - 71.93: 43 71.93 - 107.90: 4 107.90 - 143.87: 0 143.87 - 179.83: 2 Dihedral angle restraints: 2205 sinusoidal: 899 harmonic: 1306 Sorted by residual: dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O3 5RH A 601 " ideal model delta sinusoidal sigma weight residual -166.95 12.88 -179.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 5RH A 601 " pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" O2 5RH A 601 " ideal model delta sinusoidal sigma weight residual 11.42 -166.96 178.38 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual 180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 487 0.053 - 0.106: 102 0.106 - 0.160: 11 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 604 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" CA LEU A 366 " pdb=" N LEU A 366 " pdb=" C LEU A 366 " pdb=" CB LEU A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU A 61 " pdb=" N LEU A 61 " pdb=" C LEU A 61 " pdb=" CB LEU A 61 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 601 not shown) Planarity restraints: 619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " -0.096 2.00e-02 2.50e+03 1.03e-01 1.34e+02 pdb=" CG ASN A 57 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " 0.159 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.029 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" C18 5RH A 601 " 0.068 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.068 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.041 2.00e-02 2.50e+03 2.65e-02 8.76e+00 pdb=" C15 5RH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.013 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.033 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.024 2.00e-02 2.50e+03 ... (remaining 616 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 968 2.78 - 3.31: 4016 3.31 - 3.84: 5953 3.84 - 4.37: 7045 4.37 - 4.90: 11631 Nonbonded interactions: 29613 Sorted by model distance: nonbonded pdb=" OD1 ASN A 46 " pdb=" OG1 THR A 311 " model vdw 2.253 2.440 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 70 " model vdw 2.253 2.440 nonbonded pdb=" O ALA A 423 " pdb=" OG SER A 426 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR A 23 " pdb=" O ARG A 246 " model vdw 2.317 2.440 nonbonded pdb=" OE2 GLU A 225 " pdb=" N SER A 226 " model vdw 2.347 2.520 ... (remaining 29608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 1.690 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.560 Find NCS groups from input model: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.049 3660 Z= 0.373 Angle : 0.842 9.613 4990 Z= 0.502 Chirality : 0.045 0.266 604 Planarity : 0.006 0.052 618 Dihedral : 17.298 179.833 1375 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.81 % Allowed : 1.35 % Favored : 97.84 % 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: -1.23 (0.39), residues: 462 helix: -0.32 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -2.47 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 60 HIS 0.002 0.001 HIS A 284 PHE 0.021 0.002 PHE A 476 TYR 0.026 0.002 TYR A 148 ARG 0.011 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.429 Fit side-chains REVERT: A 389 PHE cc_start: 0.7591 (m-80) cc_final: 0.7004 (m-80) REVERT: A 440 TYR cc_start: 0.8101 (m-80) cc_final: 0.7515 (m-80) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.1308 time to fit residues: 12.8233 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 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 37 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3660 Z= 0.230 Angle : 0.671 9.821 4990 Z= 0.334 Chirality : 0.041 0.156 604 Planarity : 0.006 0.056 618 Dihedral : 13.076 174.937 604 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.43 % Allowed : 8.89 % Favored : 88.68 % 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: 0.31 (0.40), residues: 462 helix: 0.86 (0.29), residues: 368 sheet: None (None), residues: 0 loop : -2.26 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.003 0.001 HIS A 284 PHE 0.015 0.002 PHE A 336 TYR 0.008 0.001 TYR A 56 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.401 Fit side-chains REVERT: A 286 GLN cc_start: 0.7121 (mp10) cc_final: 0.6890 (mp10) REVERT: A 389 PHE cc_start: 0.7612 (m-80) cc_final: 0.7142 (m-80) REVERT: A 440 TYR cc_start: 0.8211 (m-80) cc_final: 0.7663 (m-80) outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.1395 time to fit residues: 13.1988 Evaluate side-chains 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3660 Z= 0.184 Angle : 0.613 9.606 4990 Z= 0.304 Chirality : 0.039 0.152 604 Planarity : 0.006 0.053 618 Dihedral : 12.302 165.997 603 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 14.56 % Favored : 83.29 % 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: 0.53 (0.41), residues: 462 helix: 0.92 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -2.01 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 250 HIS 0.002 0.000 HIS A 284 PHE 0.014 0.001 PHE A 336 TYR 0.007 0.001 TYR A 148 ARG 0.001 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.404 Fit side-chains REVERT: A 116 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7860 (m-40) REVERT: A 389 PHE cc_start: 0.7434 (m-80) cc_final: 0.7166 (m-80) REVERT: A 440 TYR cc_start: 0.8141 (m-80) cc_final: 0.7596 (m-80) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.1380 time to fit residues: 12.8844 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3660 Z= 0.199 Angle : 0.595 10.003 4990 Z= 0.295 Chirality : 0.039 0.140 604 Planarity : 0.006 0.053 618 Dihedral : 12.059 162.868 603 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.70 % Allowed : 17.52 % Favored : 79.78 % 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: 0.49 (0.40), residues: 462 helix: 0.91 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -2.07 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.010 0.001 PHE A 336 TYR 0.015 0.001 TYR A 148 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.407 Fit side-chains REVERT: A 389 PHE cc_start: 0.7408 (m-80) cc_final: 0.7187 (m-80) REVERT: A 440 TYR cc_start: 0.8159 (m-80) cc_final: 0.7571 (m-80) REVERT: A 466 LEU cc_start: 0.8598 (pp) cc_final: 0.8125 (mp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1367 time to fit residues: 10.8745 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3660 Z= 0.217 Angle : 0.585 10.188 4990 Z= 0.292 Chirality : 0.039 0.137 604 Planarity : 0.006 0.055 618 Dihedral : 11.679 157.853 603 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.77 % Allowed : 17.25 % Favored : 78.98 % 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 (0.40), residues: 462 helix: 0.97 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.97 (0.61), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.014 0.001 PHE A 476 TYR 0.011 0.001 TYR A 148 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.432 Fit side-chains REVERT: A 367 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7174 (ttm) REVERT: A 440 TYR cc_start: 0.8153 (m-80) cc_final: 0.7584 (m-80) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.1340 time to fit residues: 12.1674 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3660 Z= 0.200 Angle : 0.590 10.528 4990 Z= 0.291 Chirality : 0.039 0.133 604 Planarity : 0.006 0.056 618 Dihedral : 10.957 147.117 603 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.04 % Allowed : 19.68 % Favored : 76.28 % 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: 0.63 (0.41), residues: 462 helix: 0.99 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.98 (0.60), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.013 0.001 PHE A 336 TYR 0.009 0.001 TYR A 148 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.397 Fit side-chains REVERT: A 167 HIS cc_start: 0.8159 (p90) cc_final: 0.7924 (p90) REVERT: A 440 TYR cc_start: 0.8123 (m-80) cc_final: 0.7575 (m-80) outliers start: 15 outliers final: 8 residues processed: 69 average time/residue: 0.1330 time to fit residues: 11.8384 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3660 Z= 0.199 Angle : 0.578 10.569 4990 Z= 0.289 Chirality : 0.038 0.137 604 Planarity : 0.006 0.056 618 Dihedral : 9.652 124.643 603 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.04 % Allowed : 19.41 % Favored : 76.55 % 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: 0.66 (0.40), residues: 462 helix: 1.00 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.93 (0.61), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.010 0.001 PHE A 336 TYR 0.008 0.001 TYR A 148 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.425 Fit side-chains REVERT: A 167 HIS cc_start: 0.8146 (p90) cc_final: 0.7904 (p90) REVERT: A 367 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7157 (ttm) REVERT: A 440 TYR cc_start: 0.8155 (m-80) cc_final: 0.7597 (m-80) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.1317 time to fit residues: 11.6354 Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 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 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3660 Z= 0.205 Angle : 0.580 10.639 4990 Z= 0.291 Chirality : 0.039 0.135 604 Planarity : 0.006 0.056 618 Dihedral : 9.395 121.038 603 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.50 % Allowed : 20.22 % Favored : 76.28 % 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 (0.40), residues: 462 helix: 1.01 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.92 (0.62), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.018 0.001 PHE A 432 TYR 0.008 0.001 TYR A 148 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.416 Fit side-chains REVERT: A 367 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7169 (ttm) REVERT: A 440 TYR cc_start: 0.8160 (m-80) cc_final: 0.7615 (m-80) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1382 time to fit residues: 12.0722 Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0040 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3660 Z= 0.193 Angle : 0.580 10.629 4990 Z= 0.291 Chirality : 0.038 0.131 604 Planarity : 0.006 0.057 618 Dihedral : 9.212 118.999 603 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.50 % Allowed : 21.29 % Favored : 75.20 % 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: 0.78 (0.40), residues: 462 helix: 1.06 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -1.70 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.017 0.001 PHE A 432 TYR 0.007 0.001 TYR A 148 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.417 Fit side-chains REVERT: A 167 HIS cc_start: 0.8128 (p90) cc_final: 0.7878 (p90) REVERT: A 367 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7164 (ttm) REVERT: A 440 TYR cc_start: 0.8149 (m-80) cc_final: 0.7608 (m-80) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1388 time to fit residues: 12.2745 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3660 Z= 0.220 Angle : 0.591 10.710 4990 Z= 0.297 Chirality : 0.039 0.135 604 Planarity : 0.006 0.058 618 Dihedral : 9.191 118.911 603 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.96 % Allowed : 21.56 % Favored : 75.47 % 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 (0.40), residues: 462 helix: 1.05 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -1.67 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.016 0.001 PHE A 432 TYR 0.009 0.001 TYR A 148 ARG 0.001 0.000 ARG A 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.502 Fit side-chains REVERT: A 367 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7183 (ttm) REVERT: A 440 TYR cc_start: 0.8151 (m-80) cc_final: 0.7626 (m-80) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.1421 time to fit residues: 11.6788 Evaluate side-chains 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 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 = 0.3680 r_free = 0.3680 target = 0.142179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118869 restraints weight = 4938.855| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.08 r_work: 0.3299 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3660 Z= 0.209 Angle : 0.585 10.672 4990 Z= 0.294 Chirality : 0.039 0.135 604 Planarity : 0.006 0.059 618 Dihedral : 9.085 118.028 603 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.96 % Allowed : 21.56 % Favored : 75.47 % 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: 0.82 (0.40), residues: 462 helix: 1.09 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -1.66 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.001 0.000 HIS A 284 PHE 0.016 0.001 PHE A 432 TYR 0.008 0.001 TYR A 148 ARG 0.001 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.30 seconds wall clock time: 22 minutes 33.69 seconds (1353.69 seconds total)