Starting phenix.real_space_refine on Wed Sep 17 05:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cci_45443/09_2025/9cci_45443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cci_45443/09_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_45443/09_2025/9cci_45443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cci_45443/09_2025/9cci_45443.map" model { file = "/net/cci-nas-00/data/ceres_data/9cci_45443/09_2025/9cci_45443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cci_45443/09_2025/9cci_45443.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.52, per 1000 atoms: 0.31 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: 0.41 Conformation dependent library (CDL) restraints added in 185.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 0.81 Time building geometry restraints manager: 0.50 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: 13.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 61 TYR 0.015 0.002 TYR B 80 PHE 0.026 0.003 PHE A 377 TRP 0.021 0.002 TRP B 47 HIS 0.008 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 5056) covalent geometry : angle 0.89362 ( 6880) SS BOND : bond 0.00518 ( 7) SS BOND : angle 1.66210 ( 14) hydrogen bonds : bond 0.10913 ( 158) hydrogen bonds : angle 7.39476 ( 459) link_NAG-ASN : bond 0.00791 ( 1) link_NAG-ASN : angle 3.91381 ( 3) *********************** 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 : 0.204 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: 0.5563 time to fit residues: 61.4526 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.117230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101789 restraints weight = 7254.766| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.81 r_work: 0.3250 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5064 Z= 0.189 Angle : 0.563 7.960 6897 Z= 0.294 Chirality : 0.045 0.142 748 Planarity : 0.005 0.049 883 Dihedral : 4.922 19.794 705 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 8.93 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.33), residues: 625 helix: -2.96 (0.53), residues: 35 sheet: 0.84 (0.33), residues: 242 loop : -0.75 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.012 0.001 TYR A 380 PHE 0.011 0.002 PHE C 94 TRP 0.023 0.002 TRP B 47 HIS 0.008 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5056) covalent geometry : angle 0.56096 ( 6880) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.85605 ( 14) hydrogen bonds : bond 0.03329 ( 158) hydrogen bonds : angle 5.76737 ( 459) link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.70376 ( 3) *********************** 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 121 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8837 (ttp-170) cc_final: 0.8485 (ttm170) REVERT: C 168 THR cc_start: 0.8300 (p) cc_final: 0.8079 (m) outliers start: 10 outliers final: 3 residues processed: 113 average time/residue: 0.4888 time to fit residues: 57.9245 Evaluate side-chains 110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099094 restraints weight = 7202.475| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.79 r_work: 0.3228 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1806 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= 0.201 Angle : 0.554 7.163 6897 Z= 0.289 Chirality : 0.045 0.148 748 Planarity : 0.005 0.043 883 Dihedral : 4.878 20.315 705 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.19 % Allowed : 10.75 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.33), residues: 625 helix: -2.51 (0.61), residues: 41 sheet: 1.09 (0.34), residues: 240 loop : -0.64 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.011 0.001 TYR C 86 PHE 0.011 0.002 PHE C 94 TRP 0.020 0.002 TRP B 47 HIS 0.007 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5056) covalent geometry : angle 0.55290 ( 6880) SS BOND : bond 0.00361 ( 7) SS BOND : angle 0.87550 ( 14) hydrogen bonds : bond 0.03336 ( 158) hydrogen bonds : angle 5.59699 ( 459) link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.39008 ( 3) *********************** 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 123 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8780 (ttp-170) cc_final: 0.8481 (ttm170) REVERT: B 40 MET cc_start: 0.8598 (mmm) cc_final: 0.8093 (mtm) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.4813 time to fit residues: 58.4964 Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 195 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 46 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.0670 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 overall best weight: 0.1092 ------------------------------------------------------------------------------- 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 C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103631 restraints weight = 7192.972| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.76 r_work: 0.3280 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1896 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= 0.082 Angle : 0.482 6.579 6897 Z= 0.246 Chirality : 0.043 0.135 748 Planarity : 0.004 0.043 883 Dihedral : 4.277 17.519 705 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.37 % Allowed : 11.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.34), residues: 625 helix: -2.54 (0.56), residues: 50 sheet: 1.34 (0.33), residues: 244 loop : -0.48 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 498 TYR 0.014 0.001 TYR A 380 PHE 0.012 0.001 PHE C 135 TRP 0.009 0.001 TRP B 83 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 5056) covalent geometry : angle 0.48094 ( 6880) SS BOND : bond 0.00207 ( 7) SS BOND : angle 0.56611 ( 14) hydrogen bonds : bond 0.02682 ( 158) hydrogen bonds : angle 5.13355 ( 459) link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 1.31498 ( 3) *********************** 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 117 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.222 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.4853 time to fit residues: 55.9691 Evaluate side-chains 112 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER 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 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.0170 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 C 6 GLN C 120 GLN C 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102903 restraints weight = 7312.307| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.76 r_work: 0.3263 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1966 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= 0.117 Angle : 0.497 7.843 6897 Z= 0.254 Chirality : 0.043 0.142 748 Planarity : 0.004 0.043 883 Dihedral : 4.284 17.249 705 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.73 % Allowed : 12.20 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.34), residues: 625 helix: -2.20 (0.61), residues: 49 sheet: 1.37 (0.33), residues: 246 loop : -0.43 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.008 0.001 TYR C 86 PHE 0.010 0.001 PHE C 135 TRP 0.016 0.001 TRP B 47 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5056) covalent geometry : angle 0.49638 ( 6880) SS BOND : bond 0.00261 ( 7) SS BOND : angle 0.65720 ( 14) hydrogen bonds : bond 0.02856 ( 158) hydrogen bonds : angle 5.11887 ( 459) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 1.24250 ( 3) *********************** 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 119 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.232 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.4630 time to fit residues: 53.4966 Evaluate side-chains 111 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 100 LEU 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 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098210 restraints weight = 7349.372| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.81 r_work: 0.3212 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5064 Z= 0.257 Angle : 0.590 8.805 6897 Z= 0.302 Chirality : 0.047 0.161 748 Planarity : 0.004 0.044 883 Dihedral : 4.870 19.850 705 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.64 % Allowed : 12.39 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.34), residues: 625 helix: -2.44 (0.55), residues: 49 sheet: 1.25 (0.33), residues: 247 loop : -0.44 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.014 0.002 TYR C 86 PHE 0.013 0.002 PHE A 371 TRP 0.019 0.002 TRP B 47 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 5056) covalent geometry : angle 0.58814 ( 6880) SS BOND : bond 0.00499 ( 7) SS BOND : angle 0.97504 ( 14) hydrogen bonds : bond 0.03354 ( 158) hydrogen bonds : angle 5.47042 ( 459) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.17448 ( 3) *********************** 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 122 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8570 (mmm) cc_final: 0.8166 (mtm) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.4499 time to fit residues: 53.0455 Evaluate side-chains 112 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU 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 A residue 446 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 100 LEU 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 22 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100481 restraints weight = 7158.346| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.75 r_work: 0.3256 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2102 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= 0.110 Angle : 0.505 8.260 6897 Z= 0.256 Chirality : 0.043 0.149 748 Planarity : 0.004 0.042 883 Dihedral : 4.395 18.435 705 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.73 % Allowed : 13.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.34), residues: 625 helix: -2.49 (0.54), residues: 56 sheet: 1.28 (0.33), residues: 246 loop : -0.40 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.008 0.001 TYR B 94 PHE 0.011 0.001 PHE C 135 TRP 0.016 0.001 TRP B 47 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5056) covalent geometry : angle 0.50403 ( 6880) SS BOND : bond 0.00268 ( 7) SS BOND : angle 0.69545 ( 14) hydrogen bonds : bond 0.02844 ( 158) hydrogen bonds : angle 5.14609 ( 459) link_NAG-ASN : bond 0.00194 ( 1) link_NAG-ASN : angle 1.16934 ( 3) *********************** 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 120 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.150 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 112 average time/residue: 0.4579 time to fit residues: 53.9155 Evaluate side-chains 116 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 12 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 100 LEU 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 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.113501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098321 restraints weight = 7249.377| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.80 r_work: 0.3216 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5064 Z= 0.240 Angle : 0.583 9.466 6897 Z= 0.297 Chirality : 0.046 0.171 748 Planarity : 0.004 0.044 883 Dihedral : 4.808 20.560 705 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.46 % Allowed : 12.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.34), residues: 625 helix: -2.29 (0.56), residues: 49 sheet: 1.18 (0.33), residues: 247 loop : -0.44 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.013 0.002 TYR C 86 PHE 0.012 0.002 PHE A 371 TRP 0.020 0.002 TRP B 47 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 5056) covalent geometry : angle 0.58118 ( 6880) SS BOND : bond 0.00487 ( 7) SS BOND : angle 0.96584 ( 14) hydrogen bonds : bond 0.03287 ( 158) hydrogen bonds : angle 5.40604 ( 459) link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 1.16595 ( 3) *********************** 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 121 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8569 (mmm) cc_final: 0.8143 (mtm) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.4683 time to fit residues: 54.1426 Evaluate side-chains 114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 12 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 166 ASP 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 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099272 restraints weight = 7144.912| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.80 r_work: 0.3227 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2222 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= 0.180 Angle : 0.549 9.317 6897 Z= 0.280 Chirality : 0.045 0.168 748 Planarity : 0.004 0.042 883 Dihedral : 4.668 19.783 705 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.10 % Allowed : 12.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.34), residues: 625 helix: -2.19 (0.58), residues: 49 sheet: 1.13 (0.33), residues: 248 loop : -0.41 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.010 0.001 TYR C 86 PHE 0.010 0.001 PHE C 135 TRP 0.019 0.002 TRP B 47 HIS 0.002 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5056) covalent geometry : angle 0.54750 ( 6880) SS BOND : bond 0.00373 ( 7) SS BOND : angle 0.81853 ( 14) hydrogen bonds : bond 0.03111 ( 158) hydrogen bonds : angle 5.32582 ( 459) link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 1.11920 ( 3) *********************** 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: 17 poor density : 102 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8573 (mmm) cc_final: 0.8084 (mtm) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.4629 time to fit residues: 53.0487 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 : 0.197 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain C residue 166 ASP 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 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 overall best weight: 0.2286 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.115685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100768 restraints weight = 7274.975| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.75 r_work: 0.3259 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2235 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= 0.107 Angle : 0.518 8.938 6897 Z= 0.259 Chirality : 0.044 0.159 748 Planarity : 0.004 0.041 883 Dihedral : 4.323 17.964 705 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.73 % Allowed : 14.21 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.33), residues: 625 helix: -2.04 (0.60), residues: 50 sheet: 1.15 (0.32), residues: 248 loop : -0.31 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.011 0.001 TYR A 380 PHE 0.011 0.001 PHE C 135 TRP 0.016 0.001 TRP B 47 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5056) covalent geometry : angle 0.51746 ( 6880) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.67553 ( 14) hydrogen bonds : bond 0.02775 ( 158) hydrogen bonds : angle 5.05157 ( 459) link_NAG-ASN : bond 0.00205 ( 1) link_NAG-ASN : angle 1.17821 ( 3) ********************** 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 115 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: C 178 SER cc_start: 0.7781 (t) cc_final: 0.7575 (p) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.4907 time to fit residues: 55.5421 Evaluate side-chains 114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 356 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 166 ASP 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 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.0070 chunk 8 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.115620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100628 restraints weight = 7283.979| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.76 r_work: 0.3267 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2210 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= 0.117 Angle : 0.516 9.470 6897 Z= 0.260 Chirality : 0.043 0.158 748 Planarity : 0.004 0.042 883 Dihedral : 4.297 17.693 705 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.91 % Allowed : 14.75 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.34), residues: 625 helix: -1.91 (0.62), residues: 50 sheet: 1.18 (0.33), residues: 247 loop : -0.30 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 61 TYR 0.009 0.001 TYR C 86 PHE 0.012 0.001 PHE C 135 TRP 0.018 0.001 TRP B 47 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5056) covalent geometry : angle 0.51452 ( 6880) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.75419 ( 14) hydrogen bonds : bond 0.02845 ( 158) hydrogen bonds : angle 5.01739 ( 459) link_NAG-ASN : bond 0.00207 ( 1) link_NAG-ASN : angle 1.17819 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.98 seconds wall clock time: 47 minutes 33.16 seconds (2853.16 seconds total)