Starting phenix.real_space_refine on Sun Apr 27 14:57:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819.map" model { file = "/net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pq2_17819/04_2025/8pq2_17819_trim.cif" } resolution = 3.85 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= 0.018 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 1962 2.51 5 N 511 2.21 5 O 577 1.98 5 H 2891 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5956 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1752 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1273 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2917 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 12, 'TRANS': 177} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" 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: 4.12, per 1000 atoms: 0.69 Number of scatterers: 5956 At special positions: 0 Unit cell: (65.9412, 79.8903, 103.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 577 8.00 N 511 7.00 C 1962 6.00 H 2891 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 C 601 " - " ASN C 343 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 409.2 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 6.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.913A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.562A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.668A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.474A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.250A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG H 97 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER H 99 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG H 107 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.250A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.192A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 34 through 39 removed outlier: 6.635A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 94 hydrogen bonds defined for protein. 222 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: 1.89 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 2881 1.04 - 1.23: 89 1.23 - 1.43: 1332 1.43 - 1.63: 1726 1.63 - 1.82: 18 Bond restraints: 6046 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.94e-01 bond pdb=" C2 NAG C 601 " pdb=" N2 NAG C 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.45e-01 bond pdb=" C4 NAG C 601 " pdb=" O4 NAG C 601 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.81e-01 ... (remaining 6041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 9868 0.88 - 1.76: 883 1.76 - 2.65: 45 2.65 - 3.53: 16 3.53 - 4.41: 11 Bond angle restraints: 10823 Sorted by residual: angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" CB THR L 69 " ideal model delta sigma weight residual 113.89 109.86 4.03 1.93e+00 2.68e-01 4.35e+00 angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 124.82 121.83 2.99 1.78e+00 3.16e-01 2.83e+00 angle pdb=" C SER L 60 " pdb=" CA SER L 60 " pdb=" CB SER L 60 " ideal model delta sigma weight residual 111.50 109.34 2.16 1.29e+00 6.01e-01 2.79e+00 angle pdb=" C PHE H 33 " pdb=" N TRP H 34 " pdb=" CA TRP H 34 " ideal model delta sigma weight residual 122.77 120.73 2.04 1.41e+00 5.03e-01 2.10e+00 angle pdb=" C ALA L 43 " pdb=" CA ALA L 43 " pdb=" CB ALA L 43 " ideal model delta sigma weight residual 109.46 111.70 -2.24 1.64e+00 3.72e-01 1.87e+00 ... (remaining 10818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2773 17.34 - 34.68: 109 34.68 - 52.02: 54 52.02 - 69.36: 19 69.36 - 86.69: 3 Dihedral angle restraints: 2958 sinusoidal: 1542 harmonic: 1416 Sorted by residual: dihedral pdb=" CA PRO L 59 " pdb=" C PRO L 59 " pdb=" N SER L 60 " pdb=" CA SER L 60 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" N LYS L 39 " pdb=" CA LYS L 39 " pdb=" CB LYS L 39 " pdb=" CG LYS L 39 " ideal model delta sinusoidal sigma weight residual -60.00 -117.36 57.36 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYS L 39 " pdb=" CG LYS L 39 " pdb=" CD LYS L 39 " pdb=" CE LYS L 39 " ideal model delta sinusoidal sigma weight residual -180.00 -123.99 -56.01 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 259 0.029 - 0.058: 147 0.058 - 0.087: 21 0.087 - 0.116: 30 0.116 - 0.145: 7 Chirality restraints: 464 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL C 362 " pdb=" N VAL C 362 " pdb=" C VAL C 362 " pdb=" CB VAL C 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 461 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 337 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.07e-01 pdb=" N PRO L 59 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 36 " 0.005 2.00e-02 2.50e+03 9.23e-03 8.52e-01 pdb=" C TYR L 36 " -0.016 2.00e-02 2.50e+03 pdb=" O TYR L 36 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN L 37 " 0.005 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 345 2.20 - 2.80: 11960 2.80 - 3.40: 14397 3.40 - 4.00: 19307 4.00 - 4.60: 28938 Nonbonded interactions: 74947 Sorted by model distance: nonbonded pdb=" HE2 HIS C 339 " pdb=" O7 NAG C 601 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP H 98 " pdb=" H GLY H 108 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLN C 493 " pdb=" H SER C 494 " model vdw 1.668 2.450 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 89 " model vdw 1.670 2.450 nonbonded pdb="HH12 ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 1.690 2.450 ... (remaining 74942 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: 2.840 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.002 0.024 3161 Z= 0.112 Angle : 0.512 4.411 4314 Z= 0.265 Chirality : 0.043 0.145 464 Planarity : 0.003 0.028 551 Dihedral : 10.370 74.805 1115 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.73 % Allowed : 3.33 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.04 (0.40), residues: 384 helix: -2.37 (1.01), residues: 29 sheet: -0.21 (0.45), residues: 116 loop : -1.91 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 7 HIS 0.001 0.000 HIS C 339 PHE 0.007 0.001 PHE H 33 TYR 0.008 0.001 TYR H 94 ARG 0.001 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 0.97674 ( 3) hydrogen bonds : bond 0.08489 ( 81) hydrogen bonds : angle 5.25376 ( 222) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.97274 ( 10) covalent geometry : bond 0.00236 ( 3155) covalent geometry : angle 0.50976 ( 4301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8186 (m) cc_final: 0.7806 (p) REVERT: L 85 THR cc_start: 0.8472 (m) cc_final: 0.7972 (p) REVERT: C 353 TRP cc_start: 0.9135 (p-90) cc_final: 0.8920 (p-90) REVERT: C 474 GLN cc_start: 0.7895 (tt0) cc_final: 0.7378 (tt0) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.3497 time to fit residues: 32.7401 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093809 restraints weight = 16956.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098137 restraints weight = 8093.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101134 restraints weight = 4922.672| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3161 Z= 0.123 Angle : 0.553 4.791 4314 Z= 0.282 Chirality : 0.044 0.140 464 Planarity : 0.004 0.040 551 Dihedral : 6.866 72.864 458 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 1.82 % Allowed : 10.30 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.11 (0.40), residues: 384 helix: -3.01 (0.94), residues: 29 sheet: -0.43 (0.45), residues: 123 loop : -1.80 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS C 339 PHE 0.028 0.001 PHE H 29 TYR 0.010 0.001 TYR H 94 ARG 0.003 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 1) link_NAG-ASN : angle 1.08187 ( 3) hydrogen bonds : bond 0.03359 ( 81) hydrogen bonds : angle 4.92794 ( 222) SS BOND : bond 0.00652 ( 5) SS BOND : angle 1.66767 ( 10) covalent geometry : bond 0.00293 ( 3155) covalent geometry : angle 0.54723 ( 4301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8216 (m) cc_final: 0.7889 (p) REVERT: C 378 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7143 (ttmm) REVERT: C 474 GLN cc_start: 0.8142 (tt0) cc_final: 0.7563 (tt0) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.3047 time to fit residues: 21.2400 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092557 restraints weight = 17025.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096827 restraints weight = 8161.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099789 restraints weight = 4992.567| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3161 Z= 0.131 Angle : 0.543 5.591 4314 Z= 0.278 Chirality : 0.044 0.144 464 Planarity : 0.004 0.039 551 Dihedral : 6.847 76.831 458 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 3.33 % Allowed : 11.21 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.05 (0.40), residues: 384 helix: -2.14 (1.18), residues: 23 sheet: -0.29 (0.46), residues: 119 loop : -1.94 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS C 339 PHE 0.016 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 1) link_NAG-ASN : angle 1.01948 ( 3) hydrogen bonds : bond 0.03311 ( 81) hydrogen bonds : angle 4.91933 ( 222) SS BOND : bond 0.00483 ( 5) SS BOND : angle 1.31500 ( 10) covalent geometry : bond 0.00313 ( 3155) covalent geometry : angle 0.53979 ( 4301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8255 (m) cc_final: 0.7909 (p) REVERT: C 378 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7314 (ttmm) REVERT: C 474 GLN cc_start: 0.8200 (tt0) cc_final: 0.7939 (tt0) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.2933 time to fit residues: 20.8221 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.109362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091818 restraints weight = 17191.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096081 restraints weight = 8221.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099067 restraints weight = 5028.696| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3161 Z= 0.135 Angle : 0.545 5.810 4314 Z= 0.279 Chirality : 0.044 0.147 464 Planarity : 0.004 0.038 551 Dihedral : 6.649 76.839 457 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.64 % Allowed : 11.52 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.07 (0.40), residues: 384 helix: -2.13 (1.16), residues: 23 sheet: -0.30 (0.46), residues: 119 loop : -1.96 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS C 339 PHE 0.032 0.001 PHE H 29 TYR 0.012 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 1) link_NAG-ASN : angle 1.02467 ( 3) hydrogen bonds : bond 0.03323 ( 81) hydrogen bonds : angle 4.91112 ( 222) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.13855 ( 10) covalent geometry : bond 0.00321 ( 3155) covalent geometry : angle 0.54286 ( 4301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8261 (m) cc_final: 0.7903 (p) REVERT: C 378 LYS cc_start: 0.7670 (ttmm) cc_final: 0.7093 (ttmm) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.3830 time to fit residues: 26.1771 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091015 restraints weight = 17087.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095224 restraints weight = 8202.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098129 restraints weight = 5038.716| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3161 Z= 0.153 Angle : 0.552 5.648 4314 Z= 0.284 Chirality : 0.044 0.154 464 Planarity : 0.004 0.036 551 Dihedral : 6.294 77.572 453 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.03 % Allowed : 12.42 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.15 (0.40), residues: 384 helix: -2.22 (1.16), residues: 23 sheet: -0.39 (0.45), residues: 119 loop : -1.99 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 50 PHE 0.022 0.001 PHE H 29 TYR 0.013 0.001 TYR H 94 ARG 0.002 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 1.08787 ( 3) hydrogen bonds : bond 0.03499 ( 81) hydrogen bonds : angle 4.93590 ( 222) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.11896 ( 10) covalent geometry : bond 0.00360 ( 3155) covalent geometry : angle 0.54915 ( 4301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8274 (m) cc_final: 0.7898 (p) REVERT: C 378 LYS cc_start: 0.7667 (ttmm) cc_final: 0.7090 (ttmm) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.4092 time to fit residues: 28.8698 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091577 restraints weight = 16953.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095869 restraints weight = 8179.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098779 restraints weight = 5006.783| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.131 Angle : 0.541 5.671 4314 Z= 0.277 Chirality : 0.044 0.152 464 Planarity : 0.004 0.036 551 Dihedral : 6.233 77.648 453 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.33 % Allowed : 12.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.14 (0.40), residues: 384 helix: -2.16 (1.16), residues: 23 sheet: -0.38 (0.45), residues: 119 loop : -1.99 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS L 50 PHE 0.020 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 1) link_NAG-ASN : angle 0.95723 ( 3) hydrogen bonds : bond 0.03378 ( 81) hydrogen bonds : angle 4.92901 ( 222) SS BOND : bond 0.00386 ( 5) SS BOND : angle 1.05172 ( 10) covalent geometry : bond 0.00309 ( 3155) covalent geometry : angle 0.53878 ( 4301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8269 (m) cc_final: 0.7901 (p) REVERT: C 378 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7063 (ttmm) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.3220 time to fit residues: 22.5473 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091202 restraints weight = 17082.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095473 restraints weight = 8232.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098382 restraints weight = 5031.452| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3161 Z= 0.147 Angle : 0.552 5.491 4314 Z= 0.284 Chirality : 0.044 0.154 464 Planarity : 0.004 0.035 551 Dihedral : 6.219 77.740 453 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 3.03 % Allowed : 12.73 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.23 (0.40), residues: 384 helix: -2.22 (1.15), residues: 23 sheet: -0.43 (0.45), residues: 119 loop : -2.06 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.011 0.001 HIS L 50 PHE 0.037 0.002 PHE H 29 TYR 0.012 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 0.98870 ( 3) hydrogen bonds : bond 0.03473 ( 81) hydrogen bonds : angle 4.94841 ( 222) SS BOND : bond 0.00401 ( 5) SS BOND : angle 1.07499 ( 10) covalent geometry : bond 0.00347 ( 3155) covalent geometry : angle 0.54933 ( 4301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8277 (m) cc_final: 0.7902 (p) outliers start: 10 outliers final: 10 residues processed: 55 average time/residue: 0.3794 time to fit residues: 25.3262 Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091873 restraints weight = 16943.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096043 restraints weight = 8319.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098954 restraints weight = 5156.393| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3161 Z= 0.131 Angle : 0.542 5.469 4314 Z= 0.278 Chirality : 0.044 0.154 464 Planarity : 0.004 0.035 551 Dihedral : 6.166 77.820 453 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.03 % Allowed : 13.33 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.26 (0.40), residues: 384 helix: -2.34 (1.12), residues: 24 sheet: -0.33 (0.46), residues: 115 loop : -2.12 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS L 50 PHE 0.033 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 1) link_NAG-ASN : angle 0.91391 ( 3) hydrogen bonds : bond 0.03368 ( 81) hydrogen bonds : angle 4.90748 ( 222) SS BOND : bond 0.00377 ( 5) SS BOND : angle 0.95359 ( 10) covalent geometry : bond 0.00309 ( 3155) covalent geometry : angle 0.54051 ( 4301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8270 (m) cc_final: 0.7899 (p) outliers start: 10 outliers final: 10 residues processed: 57 average time/residue: 0.3693 time to fit residues: 25.4172 Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091130 restraints weight = 17369.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095416 restraints weight = 8285.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098411 restraints weight = 5078.291| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3161 Z= 0.139 Angle : 0.554 5.535 4314 Z= 0.284 Chirality : 0.044 0.155 464 Planarity : 0.004 0.035 551 Dihedral : 6.129 77.675 453 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.29 (0.40), residues: 384 helix: -2.35 (1.11), residues: 24 sheet: -0.34 (0.45), residues: 115 loop : -2.14 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS L 50 PHE 0.032 0.001 PHE H 29 TYR 0.012 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 1) link_NAG-ASN : angle 0.92443 ( 3) hydrogen bonds : bond 0.03399 ( 81) hydrogen bonds : angle 4.89719 ( 222) SS BOND : bond 0.00386 ( 5) SS BOND : angle 0.96283 ( 10) covalent geometry : bond 0.00331 ( 3155) covalent geometry : angle 0.55234 ( 4301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8285 (m) cc_final: 0.7891 (p) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.3624 time to fit residues: 24.5125 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091932 restraints weight = 17154.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096183 restraints weight = 8365.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099103 restraints weight = 5155.247| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.123 Angle : 0.546 5.653 4314 Z= 0.280 Chirality : 0.044 0.156 464 Planarity : 0.004 0.035 551 Dihedral : 6.067 77.678 453 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.38 % Favored : 90.36 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.28 (0.40), residues: 384 helix: -2.30 (1.12), residues: 24 sheet: -0.32 (0.45), residues: 115 loop : -2.15 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS L 50 PHE 0.031 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 1) link_NAG-ASN : angle 0.85569 ( 3) hydrogen bonds : bond 0.03292 ( 81) hydrogen bonds : angle 4.85867 ( 222) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.88842 ( 10) covalent geometry : bond 0.00293 ( 3155) covalent geometry : angle 0.54511 ( 4301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 424 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.8286 (m) cc_final: 0.7894 (p) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.3131 time to fit residues: 21.4953 Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091756 restraints weight = 17301.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096017 restraints weight = 8303.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098915 restraints weight = 5099.170| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3161 Z= 0.140 Angle : 0.570 5.608 4314 Z= 0.291 Chirality : 0.044 0.160 464 Planarity : 0.004 0.034 551 Dihedral : 6.267 77.492 453 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.68 % Favored : 89.06 % Rotamer: Outliers : 3.03 % Allowed : 13.33 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.31 (0.39), residues: 384 helix: -2.32 (1.11), residues: 24 sheet: -0.30 (0.46), residues: 115 loop : -2.19 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS L 50 PHE 0.031 0.001 PHE H 29 TYR 0.012 0.001 TYR H 94 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 1) link_NAG-ASN : angle 0.92719 ( 3) hydrogen bonds : bond 0.03316 ( 81) hydrogen bonds : angle 4.89407 ( 222) SS BOND : bond 0.00508 ( 5) SS BOND : angle 1.60225 ( 10) covalent geometry : bond 0.00332 ( 3155) covalent geometry : angle 0.56502 ( 4301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.34 seconds wall clock time: 55 minutes 13.94 seconds (3313.94 seconds total)