Starting phenix.real_space_refine on Wed Jun 4 17:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsn_32761/06_2025/7wsn_32761.cif" } resolution = 3.31 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= 0.002 sd= 0.116 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 2353 2.51 5 N 579 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3504 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} 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: 2.78, per 1000 atoms: 0.78 Number of scatterers: 3567 At special positions: 0 Unit cell: (92.0125, 58.455, 72.5275, 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 621 8.00 N 579 7.00 C 2353 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: 1.15 Conformation dependent library (CDL) restraints added in 438.6 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.634A pdb=" N GLN A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.705A pdb=" N VAL A 85 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 135 through 164 removed outlier: 3.560A pdb=" N ILE A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.742A pdb=" N THR A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.822A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Proline residue: A 212 - end of helix removed outlier: 3.631A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (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 removed outlier: 3.572A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.520A pdb=" N SER A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 6.833A pdb=" N THR A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.501A 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 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.822A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.572A pdb=" N PHE A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 446 removed outlier: 5.161A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 removed outlier: 3.504A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.689A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 542 1.31 - 1.43: 967 1.43 - 1.56: 2114 1.56 - 1.68: 1 1.68 - 1.81: 25 Bond restraints: 3649 Sorted by residual: bond pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 1.335 1.283 0.052 1.36e-02 5.41e+03 1.48e+01 bond pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.59e-02 3.96e+03 6.18e+00 bond pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N ASP A 252 " pdb=" CA ASP A 252 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.70e+00 ... (remaining 3644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 4770 1.83 - 3.66: 173 3.66 - 5.50: 28 5.50 - 7.33: 2 7.33 - 9.16: 2 Bond angle restraints: 4975 Sorted by residual: angle pdb=" N ASN A 46 " pdb=" CA ASN A 46 " pdb=" CB ASN A 46 " ideal model delta sigma weight residual 110.16 103.10 7.06 1.48e+00 4.57e-01 2.27e+01 angle pdb=" CA ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 118.48 122.63 -4.15 1.01e+00 9.80e-01 1.69e+01 angle pdb=" O ILE A 45 " pdb=" C ILE A 45 " pdb=" N ASN A 46 " ideal model delta sigma weight residual 122.12 117.65 4.47 1.16e+00 7.43e-01 1.49e+01 angle pdb=" CA ASN A 46 " pdb=" C ASN A 46 " pdb=" O ASN A 46 " ideal model delta sigma weight residual 120.42 116.59 3.83 1.06e+00 8.90e-01 1.31e+01 angle pdb=" CA SER A 412 " pdb=" C SER A 412 " pdb=" O SER A 412 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.29e+01 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 2137 35.67 - 71.33: 58 71.33 - 107.00: 3 107.00 - 142.67: 0 142.67 - 178.33: 2 Dihedral angle restraints: 2200 sinusoidal: 897 harmonic: 1303 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 193.05 14.72 178.33 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 -165.41 176.83 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 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 381 0.038 - 0.075: 169 0.075 - 0.113: 44 0.113 - 0.150: 8 0.150 - 0.188: 1 Chirality restraints: 603 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 -2.42 0.02 2.00e-02 2.50e+03 1.24e+00 chirality pdb=" CG LEU A 206 " pdb=" CB LEU A 206 " pdb=" CD1 LEU A 206 " pdb=" CD2 LEU A 206 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PHE A 336 " pdb=" N PHE A 336 " pdb=" C PHE A 336 " pdb=" CB PHE A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 600 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 57 " 0.062 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 57 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 57 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 57 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 5RH A 601 " -0.027 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C18 5RH A 601 " 0.064 2.00e-02 2.50e+03 pdb=" C19 5RH A 601 " -0.063 2.00e-02 2.50e+03 pdb=" C20 5RH A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 5RH A 601 " 0.066 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C15 5RH A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C16 5RH A 601 " 0.021 2.00e-02 2.50e+03 pdb=" C7 5RH A 601 " -0.053 2.00e-02 2.50e+03 pdb=" O1 5RH A 601 " -0.039 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 865 2.78 - 3.31: 3862 3.31 - 3.84: 5928 3.84 - 4.37: 6613 4.37 - 4.90: 11300 Nonbonded interactions: 28568 Sorted by model distance: nonbonded pdb=" OG SER A 89 " pdb=" ND2 ASN A 431 " model vdw 2.248 3.120 nonbonded pdb=" O GLY A 100 " pdb=" OG SER A 103 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" OH TYR A 440 " model vdw 2.261 3.040 nonbonded pdb=" O GLY A 92 " pdb=" OG SER A 95 " model vdw 2.372 3.040 nonbonded pdb=" NH2 ARG A 350 " pdb=" O PHE A 465 " model vdw 2.375 3.120 ... (remaining 28563 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3651 Z= 0.340 Angle : 0.840 9.162 4981 Z= 0.461 Chirality : 0.044 0.188 603 Planarity : 0.006 0.049 616 Dihedral : 17.546 178.332 1372 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.08 % Allowed : 0.27 % Favored : 98.65 % 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: -0.44 (0.39), residues: 461 helix: 0.35 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -2.88 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 202 HIS 0.004 0.001 HIS A 353 PHE 0.014 0.002 PHE A 391 TYR 0.015 0.002 TYR A 148 ARG 0.009 0.001 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00981 ( 1) link_NAG-ASN : angle 4.81094 ( 3) link_BETA1-4 : bond 0.00113 ( 1) link_BETA1-4 : angle 3.70338 ( 3) hydrogen bonds : bond 0.13925 ( 272) hydrogen bonds : angle 7.18828 ( 816) covalent geometry : bond 0.00720 ( 3649) covalent geometry : angle 0.82698 ( 4975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.379 Fit side-chains REVERT: A 264 LYS cc_start: 0.6249 (ttpt) cc_final: 0.5560 (pttm) REVERT: A 412 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (t) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1436 time to fit residues: 10.7980 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 177 GLN A 234 GLN A 299 GLN A 353 HIS A 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111122 restraints weight = 4334.501| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.11 r_work: 0.3154 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3651 Z= 0.166 Angle : 0.715 10.349 4981 Z= 0.349 Chirality : 0.043 0.195 603 Planarity : 0.005 0.047 616 Dihedral : 13.085 174.143 605 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 14.05 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.41), residues: 461 helix: 1.61 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -2.81 (0.59), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 250 HIS 0.002 0.001 HIS A 353 PHE 0.026 0.002 PHE A 463 TYR 0.022 0.002 TYR A 148 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 3.61781 ( 3) link_BETA1-4 : bond 0.00507 ( 1) link_BETA1-4 : angle 1.61497 ( 3) hydrogen bonds : bond 0.05209 ( 272) hydrogen bonds : angle 4.82821 ( 816) covalent geometry : bond 0.00358 ( 3649) covalent geometry : angle 0.70874 ( 4975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.378 Fit side-chains REVERT: A 264 LYS cc_start: 0.5499 (ttpt) cc_final: 0.5056 (pttm) REVERT: A 431 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8442 (t0) REVERT: A 434 ILE cc_start: 0.7497 (tp) cc_final: 0.7281 (tp) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1062 time to fit residues: 8.7877 Evaluate side-chains 53 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.144519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111625 restraints weight = 4313.673| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.12 r_work: 0.3158 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3651 Z= 0.151 Angle : 0.660 11.017 4981 Z= 0.323 Chirality : 0.042 0.189 603 Planarity : 0.005 0.049 616 Dihedral : 12.788 170.120 604 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 16.76 % Favored : 80.81 % 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: 1.62 (0.41), residues: 461 helix: 1.83 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.68 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.002 PHE A 336 TYR 0.016 0.001 TYR A 148 ARG 0.002 0.000 ARG A 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 3.05948 ( 3) link_BETA1-4 : bond 0.00259 ( 1) link_BETA1-4 : angle 1.91690 ( 3) hydrogen bonds : bond 0.04786 ( 272) hydrogen bonds : angle 4.58381 ( 816) covalent geometry : bond 0.00346 ( 3649) covalent geometry : angle 0.65455 ( 4975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.345 Fit side-chains REVERT: A 431 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (t0) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.1157 time to fit residues: 9.0409 Evaluate side-chains 55 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113856 restraints weight = 4196.959| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.05 r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3651 Z= 0.140 Angle : 0.631 8.346 4981 Z= 0.309 Chirality : 0.041 0.178 603 Planarity : 0.005 0.054 616 Dihedral : 12.520 166.421 604 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % 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: 1.71 (0.41), residues: 461 helix: 1.90 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.73 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.002 PHE A 336 TYR 0.014 0.001 TYR A 148 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 2.42151 ( 3) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 1.79898 ( 3) hydrogen bonds : bond 0.04469 ( 272) hydrogen bonds : angle 4.40991 ( 816) covalent geometry : bond 0.00316 ( 3649) covalent geometry : angle 0.62683 ( 4975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.336 Fit side-chains REVERT: A 104 GLN cc_start: 0.7848 (mt0) cc_final: 0.7589 (tt0) REVERT: A 431 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8431 (t0) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.1247 time to fit residues: 9.5517 Evaluate side-chains 57 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112291 restraints weight = 4259.228| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.04 r_work: 0.3140 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3651 Z= 0.155 Angle : 0.616 6.920 4981 Z= 0.307 Chirality : 0.040 0.171 603 Planarity : 0.006 0.054 616 Dihedral : 12.446 164.852 604 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 21.08 % Favored : 76.76 % 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: 1.71 (0.41), residues: 461 helix: 1.90 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.73 (0.57), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 336 TYR 0.013 0.001 TYR A 148 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 2.18736 ( 3) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.84175 ( 3) hydrogen bonds : bond 0.04610 ( 272) hydrogen bonds : angle 4.39604 ( 816) covalent geometry : bond 0.00364 ( 3649) covalent geometry : angle 0.61283 ( 4975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.347 Fit side-chains REVERT: A 104 GLN cc_start: 0.7483 (mt0) cc_final: 0.7227 (tt0) REVERT: A 431 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8350 (t0) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.1253 time to fit residues: 9.4384 Evaluate side-chains 58 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.148866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116089 restraints weight = 4262.965| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.08 r_work: 0.3202 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3651 Z= 0.126 Angle : 0.607 12.084 4981 Z= 0.293 Chirality : 0.040 0.164 603 Planarity : 0.005 0.055 616 Dihedral : 12.060 159.794 604 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.16 % Allowed : 22.16 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.41), residues: 461 helix: 2.02 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -2.63 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 353 PHE 0.015 0.001 PHE A 336 TYR 0.012 0.001 TYR A 148 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 1) link_NAG-ASN : angle 1.73373 ( 3) link_BETA1-4 : bond 0.00436 ( 1) link_BETA1-4 : angle 1.58099 ( 3) hydrogen bonds : bond 0.04097 ( 272) hydrogen bonds : angle 4.25216 ( 816) covalent geometry : bond 0.00283 ( 3649) covalent geometry : angle 0.60470 ( 4975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.348 Fit side-chains REVERT: A 104 GLN cc_start: 0.7559 (mt0) cc_final: 0.7297 (tt0) REVERT: A 431 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (t0) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.1183 time to fit residues: 9.1060 Evaluate side-chains 58 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.0270 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116335 restraints weight = 4208.190| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.06 r_work: 0.3212 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3651 Z= 0.127 Angle : 0.572 6.701 4981 Z= 0.283 Chirality : 0.039 0.130 603 Planarity : 0.005 0.055 616 Dihedral : 11.533 151.319 604 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.43 % Allowed : 23.24 % Favored : 74.32 % 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: 1.98 (0.41), residues: 461 helix: 2.06 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.49 (0.61), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 284 PHE 0.015 0.001 PHE A 336 TYR 0.012 0.001 TYR A 229 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.60566 ( 3) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.59182 ( 3) hydrogen bonds : bond 0.04098 ( 272) hydrogen bonds : angle 4.15223 ( 816) covalent geometry : bond 0.00289 ( 3649) covalent geometry : angle 0.56924 ( 4975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.343 Fit side-chains REVERT: A 104 GLN cc_start: 0.7510 (mt0) cc_final: 0.7305 (tt0) REVERT: A 431 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8373 (t0) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.1228 time to fit residues: 9.9281 Evaluate side-chains 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116573 restraints weight = 4336.390| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.16 r_work: 0.3137 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3651 Z= 0.131 Angle : 0.605 12.463 4981 Z= 0.292 Chirality : 0.039 0.153 603 Planarity : 0.005 0.059 616 Dihedral : 10.576 134.544 604 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.70 % Allowed : 23.24 % Favored : 74.05 % 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: 1.97 (0.41), residues: 461 helix: 2.06 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.53 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.001 0.000 HIS A 167 PHE 0.016 0.001 PHE A 336 TYR 0.013 0.001 TYR A 229 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.56821 ( 3) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.55557 ( 3) hydrogen bonds : bond 0.04099 ( 272) hydrogen bonds : angle 4.17666 ( 816) covalent geometry : bond 0.00304 ( 3649) covalent geometry : angle 0.60246 ( 4975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.348 Fit side-chains REVERT: A 431 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (t0) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1176 time to fit residues: 9.0635 Evaluate side-chains 56 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116190 restraints weight = 4325.954| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.19 r_work: 0.3131 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3651 Z= 0.135 Angle : 0.595 13.010 4981 Z= 0.290 Chirality : 0.039 0.164 603 Planarity : 0.005 0.058 616 Dihedral : 9.221 111.738 604 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.43 % Allowed : 23.78 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 461 helix: 2.09 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.54 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.000 0.000 HIS A 167 PHE 0.016 0.001 PHE A 336 TYR 0.013 0.001 TYR A 229 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00016 ( 1) link_NAG-ASN : angle 1.51550 ( 3) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 1.55851 ( 3) hydrogen bonds : bond 0.04133 ( 272) hydrogen bonds : angle 4.19631 ( 816) covalent geometry : bond 0.00317 ( 3649) covalent geometry : angle 0.59332 ( 4975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.342 Fit side-chains REVERT: A 104 GLN cc_start: 0.7255 (tt0) cc_final: 0.6939 (tt0) REVERT: A 431 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8426 (t0) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.1189 time to fit residues: 8.7827 Evaluate side-chains 57 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.150047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116324 restraints weight = 4364.206| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.19 r_work: 0.3176 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3651 Z= 0.136 Angle : 0.592 12.573 4981 Z= 0.289 Chirality : 0.039 0.161 603 Planarity : 0.005 0.060 616 Dihedral : 8.995 109.800 604 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 23.78 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 461 helix: 2.13 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.52 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 202 HIS 0.000 0.000 HIS A 167 PHE 0.016 0.001 PHE A 336 TYR 0.014 0.001 TYR A 229 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.49812 ( 3) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.54337 ( 3) hydrogen bonds : bond 0.04181 ( 272) hydrogen bonds : angle 4.15644 ( 816) covalent geometry : bond 0.00319 ( 3649) covalent geometry : angle 0.58984 ( 4975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.390 Fit side-chains REVERT: A 104 GLN cc_start: 0.7314 (tt0) cc_final: 0.6952 (tt0) REVERT: A 413 GLN cc_start: 0.7437 (tp40) cc_final: 0.6957 (pm20) REVERT: A 431 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (t0) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1298 time to fit residues: 8.9798 Evaluate side-chains 53 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.147394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113907 restraints weight = 4351.309| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.16 r_work: 0.3102 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3651 Z= 0.160 Angle : 0.614 12.528 4981 Z= 0.301 Chirality : 0.040 0.161 603 Planarity : 0.006 0.063 616 Dihedral : 9.029 110.647 604 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 23.24 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 461 helix: 2.10 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -2.58 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 404 HIS 0.000 0.000 HIS A 353 PHE 0.016 0.001 PHE A 336 TYR 0.013 0.001 TYR A 229 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 1.61803 ( 3) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 1.69946 ( 3) hydrogen bonds : bond 0.04555 ( 272) hydrogen bonds : angle 4.27283 ( 816) covalent geometry : bond 0.00382 ( 3649) covalent geometry : angle 0.61160 ( 4975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.30 seconds wall clock time: 36 minutes 13.16 seconds (2173.16 seconds total)