Starting phenix.real_space_refine on Sat May 10 04:04:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.map" model { file = "/net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cci_45443/05_2025/9cci_45443.cif" } resolution = 2.65 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= 0.013 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 19 5.16 5 C 3132 2.51 5 N 816 2.21 5 O 954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4921 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 212} Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 14, 'TRANS': 182} Chain: "C" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1609 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} 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: 5.68, per 1000 atoms: 1.15 Number of scatterers: 4921 At special positions: 0 Unit cell: (72.6, 97.35, 142.725, 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 19 16.00 O 954 8.00 N 816 7.00 C 3132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 190 " 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 331 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 592.0 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 10.5% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.869A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.854A pdb=" N THR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.984A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.929A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.633A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.894A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.125A pdb=" N HIS C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.612A pdb=" N LEU B 18 " --> pdb=" O TRP B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.652A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.079A pdb=" N PHE B 114 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 136 removed outlier: 5.956A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 136 removed outlier: 5.956A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 166 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.783A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.533A pdb=" N LEU C 11 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.585A pdb=" N ASN C 133 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 129 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR C 169 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 150 through 151 removed outlier: 4.703A pdb=" N TRP C 144 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 192 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 201 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 150 through 151 removed outlier: 4.703A pdb=" N TRP C 144 " --> pdb=" O GLN C 151 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 459 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: 1.49 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1534 1.34 - 1.46: 1338 1.46 - 1.58: 2161 1.58 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 5056 Sorted by residual: bond pdb=" CA SER B 125 " pdb=" CB SER B 125 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N SER B 127 " pdb=" CA SER B 127 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.15e-02 7.56e+03 9.93e+00 bond pdb=" CA SER B 124 " pdb=" CB SER B 124 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.78e-02 3.16e+03 9.44e+00 bond pdb=" N THR C 105 " pdb=" CA THR C 105 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.51e+00 ... (remaining 5051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 6632 2.11 - 4.22: 201 4.22 - 6.33: 38 6.33 - 8.44: 4 8.44 - 10.55: 5 Bond angle restraints: 6880 Sorted by residual: angle pdb=" C HIS B 212 " pdb=" N LYS B 213 " pdb=" CA LYS B 213 " ideal model delta sigma weight residual 120.09 128.15 -8.06 1.25e+00 6.40e-01 4.16e+01 angle pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " pdb=" CG ASN A 343 " ideal model delta sigma weight residual 112.60 116.67 -4.07 1.00e+00 1.00e+00 1.66e+01 angle pdb=" CA THR C 105 " pdb=" C THR C 105 " pdb=" O THR C 105 " ideal model delta sigma weight residual 121.81 117.02 4.79 1.18e+00 7.18e-01 1.65e+01 angle pdb=" CA THR C 105 " pdb=" C THR C 105 " pdb=" N VAL C 106 " ideal model delta sigma weight residual 115.27 119.90 -4.63 1.30e+00 5.92e-01 1.27e+01 angle pdb=" CA TYR C 136 " pdb=" C TYR C 136 " pdb=" N PRO C 137 " ideal model delta sigma weight residual 118.44 123.85 -5.41 1.59e+00 3.96e-01 1.16e+01 ... (remaining 6875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 2685 14.49 - 28.99: 247 28.99 - 43.48: 60 43.48 - 57.98: 12 57.98 - 72.47: 5 Dihedral angle restraints: 3009 sinusoidal: 1176 harmonic: 1833 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.61 -64.61 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA ILE C 48 " pdb=" C ILE C 48 " pdb=" N TYR C 49 " pdb=" CA TYR C 49 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLU B 108 " pdb=" C GLU B 108 " pdb=" N ASP B 109 " pdb=" CA ASP B 109 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 634 0.081 - 0.162: 101 0.162 - 0.242: 11 0.242 - 0.323: 1 0.323 - 0.404: 1 Chirality restraints: 748 Sorted by residual: chirality pdb=" CG LEU B 136 " pdb=" CB LEU B 136 " pdb=" CD1 LEU B 136 " pdb=" CD2 LEU B 136 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA ASN A 343 " pdb=" N ASN A 343 " pdb=" C ASN A 343 " pdb=" CB ASN A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C 48 " pdb=" CA ILE C 48 " pdb=" CG1 ILE C 48 " pdb=" CG2 ILE C 48 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 745 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 79 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO C 80 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO A 463 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 87 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1582 2.85 - 3.36: 3517 3.36 - 3.87: 8404 3.87 - 4.39: 9172 4.39 - 4.90: 16169 Nonbonded interactions: 38844 Sorted by model distance: nonbonded pdb=" OG1 THR B 147 " pdb=" O VAL B 196 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" OE1 GLU B 108 " model vdw 2.362 3.040 nonbonded pdb=" OE1 GLN B 23 " pdb=" OG SER B 77 " model vdw 2.380 3.040 nonbonded pdb=" O SER C 167 " pdb=" OG SER C 167 " model vdw 2.386 3.040 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.411 3.040 ... (remaining 38839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.520 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.950 Find NCS groups from input model: 0.080 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.005 0.070 5064 Z= 0.257 Angle : 0.899 10.550 6897 Z= 0.499 Chirality : 0.060 0.404 748 Planarity : 0.009 0.070 883 Dihedral : 12.275 72.470 1818 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.25 (0.31), residues: 625 helix: -4.68 (0.18), residues: 42 sheet: 0.59 (0.33), residues: 240 loop : -1.40 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 47 HIS 0.008 0.001 HIS A 339 PHE 0.026 0.003 PHE A 377 TYR 0.015 0.002 TYR B 80 ARG 0.007 0.001 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 1) link_NAG-ASN : angle 3.91381 ( 3) hydrogen bonds : bond 0.10913 ( 158) hydrogen bonds : angle 7.39476 ( 459) SS BOND : bond 0.00518 ( 7) SS BOND : angle 1.66210 ( 14) covalent geometry : bond 0.00528 ( 5056) covalent geometry : angle 0.89362 ( 6880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 6 GLN cc_start: 0.7929 (mt0) cc_final: 0.7702 (mt0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 1.0024 time to fit residues: 111.1469 Evaluate side-chains 97 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.0050 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104281 restraints weight = 7212.553| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.79 r_work: 0.3289 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5064 Z= 0.113 Angle : 0.515 7.544 6897 Z= 0.266 Chirality : 0.043 0.135 748 Planarity : 0.005 0.048 883 Dihedral : 4.610 18.361 705 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.82 % Allowed : 8.56 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.42 (0.33), residues: 625 helix: -3.18 (0.48), residues: 41 sheet: 0.91 (0.33), residues: 240 loop : -0.78 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 47 HIS 0.008 0.001 HIS A 339 PHE 0.008 0.001 PHE C 135 TYR 0.013 0.001 TYR A 380 ARG 0.005 0.000 ARG C 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 1) link_NAG-ASN : angle 1.71439 ( 3) hydrogen bonds : bond 0.02973 ( 158) hydrogen bonds : angle 5.53957 ( 459) SS BOND : bond 0.00255 ( 7) SS BOND : angle 0.67866 ( 14) covalent geometry : bond 0.00259 ( 5056) covalent geometry : angle 0.51319 ( 6880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8524 (ttm170) outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 0.9581 time to fit residues: 111.4582 Evaluate side-chains 103 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain A residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 6 GLN C 120 GLN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097898 restraints weight = 7191.875| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.80 r_work: 0.3208 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 5064 Z= 0.308 Angle : 0.630 7.856 6897 Z= 0.327 Chirality : 0.048 0.160 748 Planarity : 0.005 0.046 883 Dihedral : 5.242 21.256 705 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.55 % Allowed : 10.93 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.20 (0.33), residues: 625 helix: -2.49 (0.61), residues: 41 sheet: 0.99 (0.33), residues: 242 loop : -0.65 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 47 HIS 0.006 0.002 HIS A 339 PHE 0.015 0.002 PHE A 371 TYR 0.016 0.002 TYR C 86 ARG 0.003 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 1.32870 ( 3) hydrogen bonds : bond 0.03727 ( 158) hydrogen bonds : angle 5.80729 ( 459) SS BOND : bond 0.00549 ( 7) SS BOND : angle 1.04200 ( 14) covalent geometry : bond 0.00735 ( 5056) covalent geometry : angle 0.62866 ( 6880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8795 (ttp-170) cc_final: 0.8475 (ttm170) REVERT: B 40 MET cc_start: 0.8583 (mmm) cc_final: 0.8190 (mtm) outliers start: 14 outliers final: 6 residues processed: 113 average time/residue: 0.9382 time to fit residues: 111.6905 Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN A 409 GLN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098631 restraints weight = 7188.811| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.79 r_work: 0.3222 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5064 Z= 0.205 Angle : 0.561 7.170 6897 Z= 0.290 Chirality : 0.046 0.154 748 Planarity : 0.004 0.043 883 Dihedral : 4.917 19.869 705 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 11.11 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.33), residues: 625 helix: -2.94 (0.47), residues: 55 sheet: 1.17 (0.34), residues: 238 loop : -0.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.006 0.001 HIS A 339 PHE 0.011 0.002 PHE C 94 TYR 0.011 0.001 TYR C 86 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 1.29401 ( 3) hydrogen bonds : bond 0.03300 ( 158) hydrogen bonds : angle 5.57546 ( 459) SS BOND : bond 0.00410 ( 7) SS BOND : angle 0.87754 ( 14) covalent geometry : bond 0.00485 ( 5056) covalent geometry : angle 0.55975 ( 6880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8788 (ttp-170) cc_final: 0.8479 (ttm170) REVERT: B 40 MET cc_start: 0.8565 (mmm) cc_final: 0.8149 (mtm) REVERT: C 104 ARG cc_start: 0.8510 (ptm160) cc_final: 0.8067 (ptm160) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.9249 time to fit residues: 107.8426 Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 27 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 120 GLN C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099287 restraints weight = 7221.979| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.80 r_work: 0.3232 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5064 Z= 0.155 Angle : 0.524 7.087 6897 Z= 0.271 Chirality : 0.044 0.151 748 Planarity : 0.004 0.043 883 Dihedral : 4.657 19.396 705 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 11.84 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.07 (0.33), residues: 625 helix: -2.72 (0.51), residues: 56 sheet: 1.23 (0.33), residues: 238 loop : -0.49 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 47 HIS 0.006 0.001 HIS A 339 PHE 0.012 0.001 PHE C 135 TYR 0.009 0.001 TYR C 86 ARG 0.001 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.22672 ( 3) hydrogen bonds : bond 0.03105 ( 158) hydrogen bonds : angle 5.36717 ( 459) SS BOND : bond 0.00319 ( 7) SS BOND : angle 0.75248 ( 14) covalent geometry : bond 0.00365 ( 5056) covalent geometry : angle 0.52302 ( 6880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8570 (mmm) cc_final: 0.8066 (mtm) REVERT: B 136 LEU cc_start: 0.7648 (mt) cc_final: 0.7375 (mp) REVERT: C 6 GLN cc_start: 0.8344 (mt0) cc_final: 0.8107 (mt0) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.9552 time to fit residues: 111.3448 Evaluate side-chains 114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 120 GLN C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099755 restraints weight = 7192.429| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.78 r_work: 0.3241 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5064 Z= 0.133 Angle : 0.521 7.169 6897 Z= 0.266 Chirality : 0.044 0.153 748 Planarity : 0.004 0.042 883 Dihedral : 4.526 18.759 705 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.37 % Allowed : 13.84 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.00 (0.34), residues: 625 helix: -2.68 (0.50), residues: 56 sheet: 1.22 (0.33), residues: 246 loop : -0.44 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 47 HIS 0.004 0.001 HIS A 339 PHE 0.012 0.001 PHE C 135 TYR 0.013 0.001 TYR A 380 ARG 0.006 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 1.23657 ( 3) hydrogen bonds : bond 0.02952 ( 158) hydrogen bonds : angle 5.24416 ( 459) SS BOND : bond 0.00292 ( 7) SS BOND : angle 0.70534 ( 14) covalent geometry : bond 0.00315 ( 5056) covalent geometry : angle 0.51959 ( 6880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 6 GLN cc_start: 0.8316 (mt0) cc_final: 0.8068 (mt0) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.9224 time to fit residues: 101.8856 Evaluate side-chains 109 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 120 GLN C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099265 restraints weight = 7150.652| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.79 r_work: 0.3227 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5064 Z= 0.181 Angle : 0.539 7.720 6897 Z= 0.277 Chirality : 0.045 0.159 748 Planarity : 0.004 0.043 883 Dihedral : 4.666 19.592 705 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.73 % Allowed : 13.11 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.08 (0.34), residues: 625 helix: -2.35 (0.56), residues: 49 sheet: 1.15 (0.33), residues: 248 loop : -0.40 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 47 HIS 0.003 0.001 HIS A 339 PHE 0.010 0.001 PHE C 135 TYR 0.011 0.001 TYR C 86 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 1.21981 ( 3) hydrogen bonds : bond 0.03126 ( 158) hydrogen bonds : angle 5.34824 ( 459) SS BOND : bond 0.00364 ( 7) SS BOND : angle 0.81107 ( 14) covalent geometry : bond 0.00432 ( 5056) covalent geometry : angle 0.53752 ( 6880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8566 (mmm) cc_final: 0.8088 (mtm) REVERT: B 136 LEU cc_start: 0.7649 (mt) cc_final: 0.7355 (mp) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.8962 time to fit residues: 103.0670 Evaluate side-chains 110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098102 restraints weight = 7283.449| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.78 r_work: 0.3212 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5064 Z= 0.249 Angle : 0.582 8.116 6897 Z= 0.301 Chirality : 0.047 0.174 748 Planarity : 0.004 0.044 883 Dihedral : 4.923 20.598 705 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.91 % Allowed : 14.21 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.02 (0.34), residues: 625 helix: -2.52 (0.53), residues: 49 sheet: 1.14 (0.33), residues: 247 loop : -0.49 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.004 0.001 HIS C 194 PHE 0.013 0.002 PHE A 371 TYR 0.014 0.002 TYR C 86 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.16993 ( 3) hydrogen bonds : bond 0.03349 ( 158) hydrogen bonds : angle 5.47923 ( 459) SS BOND : bond 0.00479 ( 7) SS BOND : angle 0.98426 ( 14) covalent geometry : bond 0.00596 ( 5056) covalent geometry : angle 0.58087 ( 6880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8558 (mmm) cc_final: 0.8158 (mtm) REVERT: C 6 GLN cc_start: 0.8419 (mt0) cc_final: 0.8186 (mt0) outliers start: 16 outliers final: 12 residues processed: 111 average time/residue: 0.8946 time to fit residues: 104.8965 Evaluate side-chains 114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 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 409 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098451 restraints weight = 7173.598| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.77 r_work: 0.3219 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5064 Z= 0.212 Angle : 0.567 8.034 6897 Z= 0.290 Chirality : 0.046 0.175 748 Planarity : 0.004 0.043 883 Dihedral : 4.845 20.325 705 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.91 % Allowed : 14.39 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.04 (0.33), residues: 625 helix: -2.45 (0.54), residues: 49 sheet: 1.06 (0.32), residues: 248 loop : -0.47 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 47 HIS 0.003 0.001 HIS C 194 PHE 0.011 0.002 PHE C 135 TYR 0.012 0.001 TYR B 157 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 1.16978 ( 3) hydrogen bonds : bond 0.03246 ( 158) hydrogen bonds : angle 5.45441 ( 459) SS BOND : bond 0.00408 ( 7) SS BOND : angle 0.87765 ( 14) covalent geometry : bond 0.00507 ( 5056) covalent geometry : angle 0.56593 ( 6880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8548 (mmm) cc_final: 0.8137 (mtm) REVERT: C 6 GLN cc_start: 0.8390 (mt0) cc_final: 0.8161 (mt0) outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 0.8662 time to fit residues: 99.6770 Evaluate side-chains 114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098017 restraints weight = 7197.109| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.77 r_work: 0.3211 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5064 Z= 0.249 Angle : 0.593 8.309 6897 Z= 0.303 Chirality : 0.047 0.154 748 Planarity : 0.004 0.043 883 Dihedral : 4.953 20.654 705 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.55 % Allowed : 15.30 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.33), residues: 625 helix: -2.55 (0.52), residues: 49 sheet: 1.07 (0.33), residues: 239 loop : -0.52 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.004 0.001 HIS C 194 PHE 0.013 0.002 PHE A 371 TYR 0.014 0.002 TYR C 86 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 1.19195 ( 3) hydrogen bonds : bond 0.03364 ( 158) hydrogen bonds : angle 5.49599 ( 459) SS BOND : bond 0.00463 ( 7) SS BOND : angle 1.00403 ( 14) covalent geometry : bond 0.00597 ( 5056) covalent geometry : angle 0.59102 ( 6880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8550 (mmm) cc_final: 0.8154 (mtm) REVERT: C 6 GLN cc_start: 0.8401 (mt0) cc_final: 0.8171 (mt0) outliers start: 14 outliers final: 12 residues processed: 110 average time/residue: 0.8589 time to fit residues: 99.6730 Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.0020 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.0050 chunk 19 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 46 optimal weight: 0.0870 overall best weight: 0.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101742 restraints weight = 7241.524| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.75 r_work: 0.3274 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5064 Z= 0.083 Angle : 0.498 7.388 6897 Z= 0.249 Chirality : 0.043 0.132 748 Planarity : 0.004 0.040 883 Dihedral : 4.263 17.787 705 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.55 % Allowed : 14.75 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.11 (0.33), residues: 625 helix: -2.24 (0.58), residues: 50 sheet: 1.17 (0.32), residues: 245 loop : -0.37 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.001 0.000 HIS B 212 PHE 0.013 0.001 PHE C 135 TYR 0.005 0.001 TYR A 451 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 1.22222 ( 3) hydrogen bonds : bond 0.02678 ( 158) hydrogen bonds : angle 5.04371 ( 459) SS BOND : bond 0.00210 ( 7) SS BOND : angle 0.74975 ( 14) covalent geometry : bond 0.00192 ( 5056) covalent geometry : angle 0.49701 ( 6880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5247.72 seconds wall clock time: 91 minutes 30.27 seconds (5490.27 seconds total)