Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:51:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsm_32760/11_2022/7wsm_32760_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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 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: 2.62, 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: 1.83 Conformation dependent library (CDL) restraints added in 732.7 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: 3.36 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: 0.94 Time building geometry restraints manager: 1.90 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=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 1.617 1.321 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C27 5RH A 601 " pdb=" C28 5RH A 601 " ideal model delta sigma weight residual 1.583 1.315 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C2 5RH A 601 " pdb=" C3 5RH A 601 " ideal model delta sigma weight residual 1.697 1.513 0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C7 5RH A 601 " pdb=" C8 5RH A 601 " ideal model delta sigma weight residual 1.392 1.528 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" N 5RH A 601 " pdb=" C7 5RH A 601 " ideal model delta sigma weight residual 1.583 1.450 0.133 2.00e-02 2.50e+03 4.39e+01 ... (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=" C1 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C3 5RH A 601 " ideal model delta sigma weight residual 69.02 125.44 -56.42 3.00e+00 1.11e-01 3.54e+02 angle pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " pdb=" C20 5RH A 601 " ideal model delta sigma weight residual 85.77 125.83 -40.06 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C1 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C30 5RH A 601 " ideal model delta sigma weight residual 150.15 120.07 30.08 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C17 5RH A 601 " pdb=" C18 5RH A 601 " pdb=" C19 5RH A 601 " ideal model delta sigma weight residual 154.32 125.61 28.71 3.00e+00 1.11e-01 9.16e+01 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 ... (remaining 4985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 1861 18.64 - 37.28: 217 37.28 - 55.91: 27 55.91 - 74.55: 6 74.55 - 93.19: 5 Dihedral angle restraints: 2116 sinusoidal: 810 harmonic: 1306 Sorted by residual: 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 dihedral pdb=" CA PHE A 336 " pdb=" C PHE A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 235 " pdb=" C ASN A 235 " pdb=" N LEU A 236 " pdb=" CA LEU A 236 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 570 0.098 - 0.195: 28 0.195 - 0.293: 4 0.293 - 0.390: 0 0.390 - 0.488: 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=" C16 5RH A 601 " pdb=" C15 5RH A 601 " pdb=" C29 5RH A 601 " pdb=" C5 5RH A 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.86 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" C3 5RH A 601 " pdb=" C2 5RH A 601 " pdb=" C4 5RH A 601 " pdb=" C5 5RH A 601 " both_signs ideal model delta sigma weight residual False -2.83 -2.41 -0.42 2.00e-01 2.50e+01 4.44e+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 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. 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: 0.710 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: 1.780 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 15.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.011 0.296 3660 Z= 0.669 Angle : 1.468 56.420 4990 Z= 0.651 Chirality : 0.053 0.488 604 Planarity : 0.006 0.052 618 Dihedral : 15.875 93.189 1286 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 % 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 *********************** 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 outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.1202 time to fit residues: 11.8032 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0346 time to fit residues: 0.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 A 478 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3660 Z= 0.242 Angle : 0.800 20.460 4990 Z= 0.365 Chirality : 0.042 0.281 604 Planarity : 0.006 0.056 618 Dihedral : 6.126 80.967 514 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 2.16 % 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: 0.22 (0.40), residues: 462 helix: 0.74 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -2.21 (0.57), residues: 88 *********************** 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 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.450 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.1444 time to fit residues: 13.5973 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0429 time to fit residues: 1.0395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3660 Z= 0.244 Angle : 0.776 21.038 4990 Z= 0.350 Chirality : 0.041 0.215 604 Planarity : 0.006 0.053 618 Dihedral : 6.052 81.007 514 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.81 % 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: 0.46 (0.41), residues: 462 helix: 0.87 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -2.01 (0.60), residues: 86 *********************** 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 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.389 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 0.1293 time to fit residues: 11.4191 Evaluate side-chains 58 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0364 time to fit residues: 0.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1990 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= 0.192 Angle : 0.745 21.018 4990 Z= 0.334 Chirality : 0.040 0.222 604 Planarity : 0.006 0.053 618 Dihedral : 5.846 77.879 514 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.89 % 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: 0.48 (0.40), residues: 462 helix: 0.90 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -2.03 (0.58), residues: 88 *********************** 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 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.400 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1255 time to fit residues: 11.6354 Evaluate side-chains 61 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0362 time to fit residues: 0.8483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3660 Z= 0.232 Angle : 0.750 20.965 4990 Z= 0.335 Chirality : 0.041 0.220 604 Planarity : 0.006 0.053 618 Dihedral : 5.834 78.903 514 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 2.96 % 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: 0.48 (0.40), residues: 462 helix: 0.87 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.97 (0.60), residues: 85 *********************** 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 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.410 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1321 time to fit residues: 11.2975 Evaluate side-chains 58 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0429 time to fit residues: 0.9041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 23 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2303 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= 0.194 Angle : 0.749 20.984 4990 Z= 0.330 Chirality : 0.040 0.222 604 Planarity : 0.006 0.056 618 Dihedral : 5.712 77.023 514 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 2.16 % 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: 0.55 (0.41), residues: 462 helix: 0.93 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.97 (0.60), residues: 85 *********************** 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 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.447 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1265 time to fit residues: 10.3896 Evaluate side-chains 59 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0379 time to fit residues: 0.8784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 8 optimal weight: 0.0870 overall best weight: 0.1694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 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: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3660 Z= 0.179 Angle : 0.738 21.005 4990 Z= 0.327 Chirality : 0.039 0.222 604 Planarity : 0.006 0.054 618 Dihedral : 5.591 74.273 514 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.62 % 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: 0.55 (0.40), residues: 462 helix: 0.92 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.96 (0.61), residues: 85 *********************** 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: 6 poor density : 69 time to evaluate : 0.378 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.1292 time to fit residues: 11.8971 Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0383 time to fit residues: 0.7442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2563 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= 0.208 Angle : 0.759 20.915 4990 Z= 0.334 Chirality : 0.040 0.219 604 Planarity : 0.006 0.056 618 Dihedral : 5.622 75.469 514 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.08 % 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: 0.62 (0.41), residues: 462 helix: 0.97 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.90 (0.61), residues: 86 *********************** 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 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.413 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.1398 time to fit residues: 11.5743 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0380 time to fit residues: 0.7071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3660 Z= 0.190 Angle : 0.753 20.921 4990 Z= 0.334 Chirality : 0.040 0.222 604 Planarity : 0.006 0.057 618 Dihedral : 5.513 73.744 514 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.54 % 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 (0.40), residues: 462 helix: 1.03 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -1.85 (0.61), residues: 90 *********************** 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 67 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.420 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1387 time to fit residues: 11.9336 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0385 time to fit residues: 0.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2691 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= 0.216 Angle : 0.774 20.877 4990 Z= 0.344 Chirality : 0.040 0.220 604 Planarity : 0.006 0.059 618 Dihedral : 5.536 74.334 514 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.27 % 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 (0.40), residues: 462 helix: 1.01 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -1.83 (0.61), residues: 88 ********************** 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 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.412 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.1350 time to fit residues: 11.1188 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0380 time to fit residues: 0.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 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 = 0.3702 r_free = 0.3702 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120875 restraints weight = 4905.660| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.14 r_work: 0.3409 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3387 rms_B_bonded: 2.00 restraints_weight: 0.1250 r_work: 0.3375 rms_B_bonded: 2.11 restraints_weight: 0.0625 r_work: 0.3362 rms_B_bonded: 2.26 restraints_weight: 0.0312 r_work: 0.3348 rms_B_bonded: 2.45 restraints_weight: 0.0156 r_work: 0.3332 rms_B_bonded: 2.68 restraints_weight: 0.0078 r_work: 0.3315 rms_B_bonded: 2.96 restraints_weight: 0.0039 r_work: 0.3297 rms_B_bonded: 3.28 restraints_weight: 0.0020 r_work: 0.3277 rms_B_bonded: 3.65 restraints_weight: 0.0010 r_work: 0.3255 rms_B_bonded: 4.09 restraints_weight: 0.0005 r_work: 0.3230 rms_B_bonded: 4.59 restraints_weight: 0.0002 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2770 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= 0.196 Angle : 0.760 20.881 4990 Z= 0.334 Chirality : 0.040 0.221 604 Planarity : 0.006 0.059 618 Dihedral : 5.452 73.209 514 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.27 % 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: 1.10 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 90 =============================================================================== Job complete usr+sys time: 1075.76 seconds wall clock time: 20 minutes 23.53 seconds (1223.53 seconds total)