Starting phenix.real_space_refine on Wed Jun 4 17:37:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_32760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_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/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_32760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_32760.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_32760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsm_32760/06_2025/7wsm_32760.cif" } 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. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 2.84, per 1000 atoms: 0.79 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 - 3.00 Amino acid : True - 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: 1.20 Conformation dependent library (CDL) restraints added in 478.4 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... Secondary structure from input PDB file: 28 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 48 through 65 removed outlier: 4.084A pdb=" N GLN A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 73 through 99 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 100 through 107 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 135 through 164 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.795A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.853A pdb=" N ILE A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 removed outlier: 4.057A pdb=" N LEU A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.265A pdb=" N ALA A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.613A pdb=" N ASP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.640A pdb=" N VAL A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) 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 321 through 344 removed outlier: 3.514A pdb=" N ALA A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 349 through 373 Processing helix chain 'A' and resid 379 through 398 removed outlier: 3.947A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.562A pdb=" N PHE A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 446 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 448 through 468 Processing helix chain 'A' and resid 475 through 483 279 hydrogen bonds defined for protein. 831 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: 0.96 Time building geometry restraints manager: 1.24 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: 0.00 - 1.92: 4803 1.92 - 3.85: 159 3.85 - 5.77: 19 5.77 - 7.69: 4 7.69 - 9.61: 5 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: 951 2.78 - 3.31: 4008 3.31 - 3.84: 5987 3.84 - 4.37: 6934 4.37 - 4.90: 11613 Nonbonded interactions: 29493 Sorted by model distance: nonbonded pdb=" OD1 ASN A 46 " pdb=" OG1 THR A 311 " model vdw 2.253 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 70 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 423 " pdb=" OG SER A 426 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 23 " pdb=" O ARG A 246 " model vdw 2.317 3.040 nonbonded pdb=" OE2 GLU A 225 " pdb=" N SER A 226 " model vdw 2.347 3.120 ... (remaining 29488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- 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 3662 Z= 0.313 Angle : 0.868 10.041 4996 Z= 0.507 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 1) link_NAG-ASN : angle 5.39832 ( 3) link_BETA1-4 : bond 0.00136 ( 1) link_BETA1-4 : angle 6.79657 ( 3) hydrogen bonds : bond 0.16237 ( 279) hydrogen bonds : angle 7.91722 ( 831) covalent geometry : bond 0.00575 ( 3660) covalent geometry : angle 0.84233 ( 4990) *********************** 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 to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.357 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: 0.1293 time to fit residues: 12.6856 Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115035 restraints weight = 4920.825| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.07 r_work: 0.3273 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3662 Z= 0.171 Angle : 0.695 7.868 4996 Z= 0.345 Chirality : 0.042 0.155 604 Planarity : 0.006 0.066 618 Dihedral : 12.981 178.389 604 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 11.05 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.41), residues: 462 helix: 1.26 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.03 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.002 0.001 HIS A 284 PHE 0.023 0.002 PHE A 336 TYR 0.011 0.002 TYR A 148 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 2.98501 ( 3) link_BETA1-4 : bond 0.00721 ( 1) link_BETA1-4 : angle 1.79983 ( 3) hydrogen bonds : bond 0.05627 ( 279) hydrogen bonds : angle 4.77089 ( 831) covalent geometry : bond 0.00380 ( 3660) covalent geometry : angle 0.69035 ( 4990) *********************** 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 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.398 Fit side-chains REVERT: A 367 MET cc_start: 0.8012 (tpt) cc_final: 0.7743 (ttm) REVERT: A 389 PHE cc_start: 0.8118 (m-80) cc_final: 0.7635 (m-80) REVERT: A 440 TYR cc_start: 0.8544 (m-80) cc_final: 0.7806 (m-80) REVERT: A 466 LEU cc_start: 0.8696 (pp) cc_final: 0.8280 (mp) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.1407 time to fit residues: 13.1740 Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118845 restraints weight = 4861.633| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.05 r_work: 0.3305 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3662 Z= 0.146 Angle : 0.641 8.829 4996 Z= 0.313 Chirality : 0.040 0.160 604 Planarity : 0.005 0.067 618 Dihedral : 12.739 174.291 603 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.23 % Allowed : 16.44 % Favored : 80.32 % 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: 1.50 (0.41), residues: 462 helix: 1.65 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.002 0.000 HIS A 284 PHE 0.011 0.001 PHE A 483 TYR 0.011 0.001 TYR A 148 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 3.01615 ( 3) link_BETA1-4 : bond 0.00178 ( 1) link_BETA1-4 : angle 1.82422 ( 3) hydrogen bonds : bond 0.04719 ( 279) hydrogen bonds : angle 4.41789 ( 831) covalent geometry : bond 0.00327 ( 3660) covalent geometry : angle 0.63579 ( 4990) *********************** 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 81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.352 Fit side-chains REVERT: A 41 ASN cc_start: 0.8691 (m110) cc_final: 0.8442 (m-40) REVERT: A 116 ASN cc_start: 0.8474 (m-40) cc_final: 0.8257 (m-40) REVERT: A 151 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8097 (mm) REVERT: A 367 MET cc_start: 0.7889 (tpt) cc_final: 0.7657 (ttm) REVERT: A 389 PHE cc_start: 0.7937 (m-80) cc_final: 0.7712 (m-80) REVERT: A 440 TYR cc_start: 0.8406 (m-80) cc_final: 0.7584 (m-80) REVERT: A 476 PHE cc_start: 0.7846 (t80) cc_final: 0.7542 (m-80) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1443 time to fit residues: 13.6512 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 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 257 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 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 29 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119083 restraints weight = 4859.159| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.08 r_work: 0.3328 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3662 Z= 0.136 Angle : 0.643 13.719 4996 Z= 0.310 Chirality : 0.040 0.157 604 Planarity : 0.005 0.069 618 Dihedral : 12.566 171.470 603 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.23 % Allowed : 17.25 % Favored : 79.51 % 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: 1.57 (0.40), residues: 462 helix: 1.63 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.90 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.002 0.000 HIS A 167 PHE 0.009 0.001 PHE A 463 TYR 0.019 0.001 TYR A 148 ARG 0.001 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 1) link_NAG-ASN : angle 2.78623 ( 3) link_BETA1-4 : bond 0.00237 ( 1) link_BETA1-4 : angle 1.57365 ( 3) hydrogen bonds : bond 0.04396 ( 279) hydrogen bonds : angle 4.35532 ( 831) covalent geometry : bond 0.00302 ( 3660) covalent geometry : angle 0.63830 ( 4990) *********************** 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 74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.411 Fit side-chains REVERT: A 116 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8176 (m-40) REVERT: A 151 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8124 (mm) REVERT: A 367 MET cc_start: 0.7882 (tpt) cc_final: 0.7633 (ttm) REVERT: A 440 TYR cc_start: 0.8398 (m-80) cc_final: 0.7570 (m-80) REVERT: A 476 PHE cc_start: 0.7794 (t80) cc_final: 0.7527 (m-80) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.1378 time to fit residues: 11.8787 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 151 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 257 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118200 restraints weight = 4985.460| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.10 r_work: 0.3300 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.039 3662 Z= 0.150 Angle : 0.644 13.930 4996 Z= 0.308 Chirality : 0.040 0.149 604 Planarity : 0.005 0.068 618 Dihedral : 12.615 172.019 603 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.85 % Allowed : 18.33 % Favored : 76.82 % 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: 1.59 (0.40), residues: 462 helix: 1.62 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.81 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.001 0.000 HIS A 167 PHE 0.015 0.001 PHE A 432 TYR 0.013 0.001 TYR A 148 ARG 0.003 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 2.51626 ( 3) link_BETA1-4 : bond 0.00255 ( 1) link_BETA1-4 : angle 1.60307 ( 3) hydrogen bonds : bond 0.04524 ( 279) hydrogen bonds : angle 4.30553 ( 831) covalent geometry : bond 0.00350 ( 3660) covalent geometry : angle 0.63972 ( 4990) *********************** 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 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.354 Fit side-chains REVERT: A 440 TYR cc_start: 0.8436 (m-80) cc_final: 0.7651 (m-80) REVERT: A 476 PHE cc_start: 0.7905 (t80) cc_final: 0.7532 (m-80) outliers start: 18 outliers final: 10 residues processed: 69 average time/residue: 0.1179 time to fit residues: 10.6572 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 257 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 339 VAL Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 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 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117796 restraints weight = 4976.900| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.10 r_work: 0.3293 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3662 Z= 0.149 Angle : 0.644 14.629 4996 Z= 0.307 Chirality : 0.040 0.150 604 Planarity : 0.005 0.069 618 Dihedral : 12.629 171.803 603 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.31 % Allowed : 20.22 % 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: 1.57 (0.40), residues: 462 helix: 1.62 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.85 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 60 HIS 0.001 0.000 HIS A 284 PHE 0.013 0.001 PHE A 432 TYR 0.010 0.001 TYR A 148 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 2.46612 ( 3) link_BETA1-4 : bond 0.00184 ( 1) link_BETA1-4 : angle 1.52607 ( 3) hydrogen bonds : bond 0.04476 ( 279) hydrogen bonds : angle 4.34024 ( 831) covalent geometry : bond 0.00347 ( 3660) covalent geometry : angle 0.64068 ( 4990) *********************** 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 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.388 Fit side-chains REVERT: A 440 TYR cc_start: 0.8496 (m-80) cc_final: 0.7716 (m-80) REVERT: A 476 PHE cc_start: 0.7915 (t80) cc_final: 0.7575 (m-80) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.1235 time to fit residues: 10.7896 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 257 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 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118950 restraints weight = 4922.886| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.08 r_work: 0.3309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3662 Z= 0.138 Angle : 0.632 14.926 4996 Z= 0.301 Chirality : 0.040 0.149 604 Planarity : 0.005 0.068 618 Dihedral : 12.514 170.130 603 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.77 % Allowed : 21.56 % Favored : 74.66 % 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: 1.63 (0.40), residues: 462 helix: 1.64 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.80 (0.62), residues: 77 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 0.015 0.001 PHE A 336 TYR 0.009 0.001 TYR A 148 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 1) link_NAG-ASN : angle 2.41819 ( 3) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 1.43156 ( 3) hydrogen bonds : bond 0.04307 ( 279) hydrogen bonds : angle 4.26750 ( 831) covalent geometry : bond 0.00319 ( 3660) covalent geometry : angle 0.62898 ( 4990) *********************** 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 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.408 Fit side-chains REVERT: A 440 TYR cc_start: 0.8512 (m-80) cc_final: 0.7747 (m-80) REVERT: A 476 PHE cc_start: 0.7901 (t80) cc_final: 0.7589 (m-80) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.1333 time to fit residues: 11.6676 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 257 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 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120344 restraints weight = 4922.921| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.08 r_work: 0.3326 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3662 Z= 0.132 Angle : 0.643 15.265 4996 Z= 0.305 Chirality : 0.040 0.148 604 Planarity : 0.005 0.068 618 Dihedral : 12.395 168.792 603 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.50 % Allowed : 22.10 % Favored : 74.39 % 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: 1.70 (0.40), residues: 462 helix: 1.70 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 60 HIS 0.000 0.000 HIS A 284 PHE 0.015 0.001 PHE A 336 TYR 0.008 0.001 TYR A 148 ARG 0.003 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 2.38546 ( 3) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 1.33607 ( 3) hydrogen bonds : bond 0.04161 ( 279) hydrogen bonds : angle 4.21329 ( 831) covalent geometry : bond 0.00297 ( 3660) covalent geometry : angle 0.63990 ( 4990) *********************** 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 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.390 Fit side-chains REVERT: A 440 TYR cc_start: 0.8522 (m-80) cc_final: 0.7814 (m-80) REVERT: A 476 PHE cc_start: 0.7812 (t80) cc_final: 0.7566 (m-80) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1273 time to fit residues: 11.2359 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 LEU Chi-restraints excluded: chain A residue 257 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 294 LEU Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120186 restraints weight = 4901.769| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.09 r_work: 0.3331 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3662 Z= 0.135 Angle : 0.646 15.772 4996 Z= 0.307 Chirality : 0.040 0.147 604 Planarity : 0.005 0.068 618 Dihedral : 12.378 168.664 603 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.50 % Allowed : 21.83 % Favored : 74.66 % 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: 1.75 (0.40), residues: 462 helix: 1.71 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.66 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 60 HIS 0.000 0.000 HIS A 284 PHE 0.015 0.001 PHE A 336 TYR 0.009 0.001 TYR A 148 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 2.29283 ( 3) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.32354 ( 3) hydrogen bonds : bond 0.04210 ( 279) hydrogen bonds : angle 4.20438 ( 831) covalent geometry : bond 0.00308 ( 3660) covalent geometry : angle 0.64298 ( 4990) *********************** 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 to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.389 Fit side-chains REVERT: A 440 TYR cc_start: 0.8524 (m-80) cc_final: 0.7818 (m-80) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 0.1286 time to fit residues: 10.8965 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 chunk 38 optimal weight: 0.0070 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121990 restraints weight = 4857.791| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.09 r_work: 0.3333 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3662 Z= 0.128 Angle : 0.651 15.907 4996 Z= 0.308 Chirality : 0.040 0.144 604 Planarity : 0.005 0.069 618 Dihedral : 12.237 166.992 603 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.96 % Allowed : 23.45 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.40), residues: 462 helix: 1.68 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -1.54 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 60 HIS 0.000 0.000 HIS A 284 PHE 0.014 0.001 PHE A 336 TYR 0.008 0.001 TYR A 148 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 2.26520 ( 3) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 1.25078 ( 3) hydrogen bonds : bond 0.04054 ( 279) hydrogen bonds : angle 4.25122 ( 831) covalent geometry : bond 0.00286 ( 3660) covalent geometry : angle 0.64803 ( 4990) ********************** 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 74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.342 Fit side-chains REVERT: A 440 TYR cc_start: 0.8524 (m-80) cc_final: 0.7804 (m-80) REVERT: A 476 PHE cc_start: 0.7787 (t80) cc_final: 0.7554 (m-80) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.1242 time to fit residues: 11.5456 Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121351 restraints weight = 4880.961| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.06 r_work: 0.3337 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3662 Z= 0.135 Angle : 0.646 15.487 4996 Z= 0.310 Chirality : 0.040 0.146 604 Planarity : 0.005 0.068 618 Dihedral : 12.257 167.317 603 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.96 % Allowed : 22.91 % Favored : 74.12 % 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: 1.75 (0.40), residues: 462 helix: 1.70 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 60 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 336 TYR 0.007 0.001 TYR A 148 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 1) link_NAG-ASN : angle 2.26563 ( 3) link_BETA1-4 : bond 0.00252 ( 1) link_BETA1-4 : angle 1.27358 ( 3) hydrogen bonds : bond 0.04139 ( 279) hydrogen bonds : angle 4.24379 ( 831) covalent geometry : bond 0.00314 ( 3660) covalent geometry : angle 0.64339 ( 4990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.80 seconds wall clock time: 38 minutes 22.51 seconds (2302.51 seconds total)