Starting phenix.real_space_refine on Wed Jul 23 16:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2025/7zr8_14886.cif" } resolution = 3.7 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= 0.000 sd= 0.012 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 18 5.16 5 C 2346 2.51 5 N 623 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3693 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 13, 'TRANS': 231} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.98, per 1000 atoms: 1.08 Number of scatterers: 3693 At special positions: 0 Unit cell: (68.06, 75.53, 111.22, 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 18 16.00 O 706 8.00 N 623 7.00 C 2346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 340 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 435.1 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 866 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 9.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.601A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.017A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.371A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.137A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.569A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.794A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.530A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.339A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1178 1.34 - 1.46: 930 1.46 - 1.58: 1653 1.58 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 3784 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.08e-01 bond pdb=" C4 NAG A1301 " pdb=" O4 NAG A1301 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.82e-01 ... (remaining 3779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 4994 1.15 - 2.31: 101 2.31 - 3.46: 37 3.46 - 4.61: 4 4.61 - 5.77: 1 Bond angle restraints: 5137 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.77 109.00 2.77 1.04e+00 9.25e-01 7.10e+00 angle pdb=" C ALA A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 121.65 119.16 2.49 1.01e+00 9.80e-01 6.07e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" CB ASP H 103 " ideal model delta sigma weight residual 113.65 110.44 3.21 1.47e+00 4.63e-01 4.78e+00 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.97 110.97 2.00 1.06e+00 8.90e-01 3.57e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 ... (remaining 5132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.18: 2044 10.18 - 20.36: 146 20.36 - 30.54: 47 30.54 - 40.72: 13 40.72 - 50.90: 5 Dihedral angle restraints: 2255 sinusoidal: 893 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 129.10 50.90 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PRO A 524 " pdb=" C PRO A 524 " pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" N TYR A 498 " pdb=" CA TYR A 498 " pdb=" CB TYR A 498 " pdb=" CG TYR A 498 " ideal model delta sinusoidal sigma weight residual -60.00 -108.10 48.10 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 340 0.030 - 0.059: 142 0.059 - 0.089: 30 0.089 - 0.118: 42 0.118 - 0.148: 4 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 399 " pdb=" N ILE A 399 " pdb=" C ILE A 399 " pdb=" CB ILE A 399 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 555 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO L 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 326 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 327 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 558 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.014 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 174 2.73 - 3.27: 3512 3.27 - 3.81: 5835 3.81 - 4.36: 7174 4.36 - 4.90: 12818 Nonbonded interactions: 29513 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.181 3.040 nonbonded pdb=" OG1 THR H 33 " pdb=" OG SER H 99 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.255 3.040 nonbonded pdb=" O LYS H 13 " pdb=" OG SER H 16 " model vdw 2.281 3.040 nonbonded pdb=" O GLN L 90 " pdb=" N GLU L 92 " model vdw 2.291 3.120 ... (remaining 29508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.003 0.028 3791 Z= 0.124 Angle : 0.466 5.767 5152 Z= 0.249 Chirality : 0.042 0.148 558 Planarity : 0.004 0.049 663 Dihedral : 8.421 50.903 1371 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.74 % Allowed : 3.71 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.42), residues: 465 helix: -3.12 (0.74), residues: 33 sheet: -0.75 (0.46), residues: 156 loop : -0.08 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 516 PHE 0.009 0.001 PHE A 426 TYR 0.009 0.001 TYR L 91 ARG 0.001 0.000 ARG A 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 1.33788 ( 3) hydrogen bonds : bond 0.24152 ( 106) hydrogen bonds : angle 11.62971 ( 252) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.33517 ( 12) covalent geometry : bond 0.00277 ( 3784) covalent geometry : angle 0.46498 ( 5137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9035 (tp) cc_final: 0.8645 (pt) REVERT: A 343 ARG cc_start: 0.9345 (mtt-85) cc_final: 0.9013 (ttm-80) REVERT: A 511 SER cc_start: 0.9440 (m) cc_final: 0.9192 (t) REVERT: A 532 LYS cc_start: 0.8724 (mttt) cc_final: 0.8496 (mttp) outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.2035 time to fit residues: 21.3405 Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.0050 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 539 ASN L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135212 restraints weight = 4335.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136167 restraints weight = 3897.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137055 restraints weight = 3608.534| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3791 Z= 0.157 Angle : 0.527 4.766 5152 Z= 0.284 Chirality : 0.044 0.149 558 Planarity : 0.004 0.044 663 Dihedral : 4.546 44.586 541 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.23 % Allowed : 11.63 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.65 (0.42), residues: 465 helix: -3.16 (0.93), residues: 28 sheet: -0.62 (0.45), residues: 153 loop : 0.11 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.021 0.001 TYR L 91 ARG 0.004 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.45195 ( 3) hydrogen bonds : bond 0.04424 ( 106) hydrogen bonds : angle 7.61217 ( 252) SS BOND : bond 0.00298 ( 6) SS BOND : angle 0.63473 ( 12) covalent geometry : bond 0.00354 ( 3784) covalent geometry : angle 0.52605 ( 5137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9089 (tp) cc_final: 0.8728 (pt) REVERT: A 343 ARG cc_start: 0.9296 (mtt-85) cc_final: 0.9053 (ttm-80) REVERT: L 38 GLN cc_start: 0.9157 (tt0) cc_final: 0.8709 (tt0) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.2233 time to fit residues: 19.4106 Evaluate side-chains 69 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.161566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135814 restraints weight = 4299.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136432 restraints weight = 3870.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137305 restraints weight = 3620.475| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3791 Z= 0.140 Angle : 0.504 5.868 5152 Z= 0.267 Chirality : 0.044 0.147 558 Planarity : 0.004 0.042 663 Dihedral : 4.621 50.964 541 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.47 % Allowed : 11.88 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.41), residues: 465 helix: -3.16 (0.90), residues: 28 sheet: -0.62 (0.43), residues: 153 loop : 0.10 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.008 0.001 PHE A 540 TYR 0.015 0.001 TYR L 91 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.42696 ( 3) hydrogen bonds : bond 0.03615 ( 106) hydrogen bonds : angle 6.76783 ( 252) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.76838 ( 12) covalent geometry : bond 0.00318 ( 3784) covalent geometry : angle 0.50179 ( 5137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9078 (tp) cc_final: 0.8780 (pt) REVERT: L 38 GLN cc_start: 0.9142 (tt0) cc_final: 0.8712 (tt0) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.1955 time to fit residues: 17.2039 Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136175 restraints weight = 4406.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136904 restraints weight = 3952.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136923 restraints weight = 3674.507| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3791 Z= 0.142 Angle : 0.497 6.181 5152 Z= 0.263 Chirality : 0.044 0.148 558 Planarity : 0.004 0.042 663 Dihedral : 4.697 56.839 541 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.72 % Allowed : 14.11 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.74 (0.41), residues: 465 helix: -3.10 (0.89), residues: 29 sheet: -0.68 (0.42), residues: 153 loop : 0.04 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.009 0.001 PHE A 426 TYR 0.014 0.001 TYR L 91 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.43134 ( 3) hydrogen bonds : bond 0.03279 ( 106) hydrogen bonds : angle 6.40887 ( 252) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.82101 ( 12) covalent geometry : bond 0.00327 ( 3784) covalent geometry : angle 0.49467 ( 5137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9070 (tp) cc_final: 0.8739 (pt) REVERT: L 38 GLN cc_start: 0.9143 (tt0) cc_final: 0.8895 (tt0) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.2027 time to fit residues: 17.1965 Evaluate side-chains 71 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134572 restraints weight = 4440.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135396 restraints weight = 3958.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135409 restraints weight = 3641.699| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3791 Z= 0.123 Angle : 0.494 6.684 5152 Z= 0.261 Chirality : 0.044 0.145 558 Planarity : 0.004 0.041 663 Dihedral : 4.636 57.294 541 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.22 % Allowed : 14.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.72 (0.41), residues: 465 helix: -3.08 (0.87), residues: 29 sheet: -0.67 (0.41), residues: 154 loop : 0.07 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.007 0.001 PHE A 540 TYR 0.013 0.001 TYR L 91 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.35302 ( 3) hydrogen bonds : bond 0.03029 ( 106) hydrogen bonds : angle 6.16824 ( 252) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.88169 ( 12) covalent geometry : bond 0.00282 ( 3784) covalent geometry : angle 0.49147 ( 5137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9057 (tp) cc_final: 0.8750 (pt) REVERT: L 38 GLN cc_start: 0.9113 (tt0) cc_final: 0.8837 (tt0) outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 0.1824 time to fit residues: 15.9195 Evaluate side-chains 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135803 restraints weight = 4392.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136750 restraints weight = 3907.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136750 restraints weight = 3589.111| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3791 Z= 0.147 Angle : 0.503 7.124 5152 Z= 0.266 Chirality : 0.044 0.146 558 Planarity : 0.004 0.040 663 Dihedral : 4.585 53.717 541 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.71 % Allowed : 12.87 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 465 helix: -2.98 (0.87), residues: 29 sheet: -0.65 (0.42), residues: 153 loop : -0.01 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.013 0.001 TYR A 470 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 1.41202 ( 3) hydrogen bonds : bond 0.03020 ( 106) hydrogen bonds : angle 6.10284 ( 252) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.89841 ( 12) covalent geometry : bond 0.00340 ( 3784) covalent geometry : angle 0.50055 ( 5137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9054 (tp) cc_final: 0.8738 (pt) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.1582 time to fit residues: 13.4907 Evaluate side-chains 71 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137032 restraints weight = 4364.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137635 restraints weight = 3898.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138644 restraints weight = 3636.344| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3791 Z= 0.159 Angle : 0.520 7.544 5152 Z= 0.274 Chirality : 0.045 0.149 558 Planarity : 0.004 0.041 663 Dihedral : 4.553 49.419 541 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.71 % Allowed : 13.61 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.77 (0.41), residues: 465 helix: -2.84 (0.90), residues: 29 sheet: -0.68 (0.41), residues: 153 loop : -0.02 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.015 0.001 TYR A 450 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 1.50349 ( 3) hydrogen bonds : bond 0.02982 ( 106) hydrogen bonds : angle 6.15948 ( 252) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.92815 ( 12) covalent geometry : bond 0.00371 ( 3784) covalent geometry : angle 0.51778 ( 5137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9054 (tp) cc_final: 0.8738 (pt) REVERT: H 112 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8312 (t) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.1877 time to fit residues: 15.6478 Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.161224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134272 restraints weight = 4425.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135362 restraints weight = 3923.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136425 restraints weight = 3597.511| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3791 Z= 0.198 Angle : 0.544 8.032 5152 Z= 0.288 Chirality : 0.045 0.155 558 Planarity : 0.004 0.040 663 Dihedral : 4.600 45.897 541 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.71 % Allowed : 13.37 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.91 (0.41), residues: 465 helix: -2.81 (0.92), residues: 29 sheet: -0.83 (0.41), residues: 154 loop : -0.09 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 108 HIS 0.002 0.001 HIS A 516 PHE 0.010 0.001 PHE A 426 TYR 0.013 0.001 TYR A 486 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.68600 ( 3) hydrogen bonds : bond 0.03080 ( 106) hydrogen bonds : angle 6.28052 ( 252) SS BOND : bond 0.00206 ( 6) SS BOND : angle 1.01084 ( 12) covalent geometry : bond 0.00463 ( 3784) covalent geometry : angle 0.54064 ( 5137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9073 (tp) cc_final: 0.8743 (pt) REVERT: A 387 LEU cc_start: 0.9113 (mt) cc_final: 0.8894 (mt) REVERT: A 389 PHE cc_start: 0.8830 (m-80) cc_final: 0.8615 (m-80) REVERT: A 562 PHE cc_start: 0.8466 (p90) cc_final: 0.7528 (p90) REVERT: A 564 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6318 (ptp90) REVERT: H 112 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8274 (t) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 0.1732 time to fit residues: 14.8503 Evaluate side-chains 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131632 restraints weight = 4321.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132414 restraints weight = 3904.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132414 restraints weight = 3605.419| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3791 Z= 0.202 Angle : 0.560 8.750 5152 Z= 0.299 Chirality : 0.046 0.155 558 Planarity : 0.004 0.040 663 Dihedral : 4.618 42.069 541 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.96 % Allowed : 14.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.03 (0.40), residues: 465 helix: -2.75 (0.93), residues: 29 sheet: -0.88 (0.41), residues: 155 loop : -0.21 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 108 HIS 0.002 0.001 HIS A 516 PHE 0.011 0.001 PHE A 426 TYR 0.013 0.001 TYR L 91 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.75468 ( 3) hydrogen bonds : bond 0.03178 ( 106) hydrogen bonds : angle 6.23606 ( 252) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.95471 ( 12) covalent geometry : bond 0.00476 ( 3784) covalent geometry : angle 0.55695 ( 5137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9082 (tp) cc_final: 0.8759 (pt) REVERT: A 387 LEU cc_start: 0.9062 (mt) cc_final: 0.8843 (mt) REVERT: A 389 PHE cc_start: 0.8842 (m-80) cc_final: 0.8614 (m-80) REVERT: A 562 PHE cc_start: 0.8434 (p90) cc_final: 0.7500 (p90) REVERT: A 564 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6408 (ptp90) REVERT: H 112 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8309 (t) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.1658 time to fit residues: 13.7313 Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 25 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137822 restraints weight = 4367.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138736 restraints weight = 3864.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139341 restraints weight = 3550.590| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3791 Z= 0.142 Angle : 0.533 8.920 5152 Z= 0.284 Chirality : 0.044 0.149 558 Planarity : 0.004 0.039 663 Dihedral : 4.352 35.038 541 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.71 % Allowed : 14.85 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.40), residues: 465 helix: -2.70 (0.94), residues: 29 sheet: -0.74 (0.41), residues: 154 loop : -0.21 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.010 0.001 PHE A 540 TYR 0.012 0.001 TYR A 486 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 1.49522 ( 3) hydrogen bonds : bond 0.02987 ( 106) hydrogen bonds : angle 6.03695 ( 252) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.90655 ( 12) covalent geometry : bond 0.00331 ( 3784) covalent geometry : angle 0.53122 ( 5137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9019 (tp) cc_final: 0.8694 (pt) REVERT: A 387 LEU cc_start: 0.8995 (mt) cc_final: 0.8781 (mt) REVERT: A 389 PHE cc_start: 0.8804 (m-80) cc_final: 0.8595 (m-80) REVERT: H 112 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8257 (t) outliers start: 15 outliers final: 13 residues processed: 62 average time/residue: 0.2265 time to fit residues: 17.7744 Evaluate side-chains 64 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.160909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135517 restraints weight = 4384.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136604 restraints weight = 3881.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137097 restraints weight = 3567.223| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3791 Z= 0.138 Angle : 0.531 9.015 5152 Z= 0.282 Chirality : 0.044 0.147 558 Planarity : 0.004 0.039 663 Dihedral : 4.181 27.364 541 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.71 % Allowed : 15.10 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.85 (0.41), residues: 465 helix: -2.65 (0.95), residues: 29 sheet: -0.63 (0.42), residues: 154 loop : -0.18 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.009 0.001 PHE A 540 TYR 0.013 0.001 TYR A 486 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 1.46949 ( 3) hydrogen bonds : bond 0.02929 ( 106) hydrogen bonds : angle 5.91233 ( 252) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.90779 ( 12) covalent geometry : bond 0.00320 ( 3784) covalent geometry : angle 0.52907 ( 5137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.99 seconds wall clock time: 41 minutes 47.39 seconds (2507.39 seconds total)