Starting phenix.real_space_refine on Tue Mar 3 11:58:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2026/7n8i_24237.map" } resolution = 3.0 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= 0.053 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 13 5.16 5 C 2315 2.51 5 N 581 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3600 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1759 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 0.98, per 1000 atoms: 0.27 Number of scatterers: 3600 At special positions: 0 Unit cell: (56.481, 85.143, 75.87, 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 13 16.00 O 691 8.00 N 581 7.00 C 2315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 282 " Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 86.3 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 9 sheets defined 5.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.867A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.910A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.381A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.609A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.625A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.944A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.090A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 369 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: 0.57 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 593 1.31 - 1.44: 1076 1.44 - 1.57: 1999 1.57 - 1.69: 6 1.69 - 1.82: 17 Bond restraints: 3691 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.89e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.45e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.585 -0.055 2.00e-02 2.50e+03 7.43e+00 ... (remaining 3686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4350 1.62 - 3.24: 543 3.24 - 4.86: 69 4.86 - 6.48: 38 6.48 - 8.10: 11 Bond angle restraints: 5011 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.12 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.42 -8.10 1.14e+00 7.69e-01 5.05e+01 angle pdb=" C TYR A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.01e+00 9.80e-01 4.49e+01 angle pdb=" C LEU A 216 " pdb=" N PRO A 217 " pdb=" CA PRO A 217 " ideal model delta sigma weight residual 119.85 126.54 -6.69 1.01e+00 9.80e-01 4.39e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.55 -6.79 1.03e+00 9.43e-01 4.35e+01 ... (remaining 5006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 2112 16.43 - 32.86: 78 32.86 - 49.29: 13 49.29 - 65.72: 10 65.72 - 82.14: 4 Dihedral angle restraints: 2217 sinusoidal: 925 harmonic: 1292 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.69 40.31 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " pdb=" CG ASN A 165 " pdb=" OD1 ASN A 165 " ideal model delta sinusoidal sigma weight residual 120.00 -168.17 -71.83 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 2214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 397 0.064 - 0.127: 121 0.127 - 0.190: 27 0.190 - 0.254: 10 0.254 - 0.317: 6 Chirality restraints: 561 Sorted by residual: chirality pdb=" C2 NAG A1303 " pdb=" C1 NAG A1303 " pdb=" C3 NAG A1303 " pdb=" N2 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C2 NAG A1305 " pdb=" C1 NAG A1305 " pdb=" C3 NAG A1305 " pdb=" N2 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 558 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.026 2.00e-02 2.50e+03 2.66e-02 8.86e+00 pdb=" CG ASN A 165 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 28 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C ASP L 28 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP L 28 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE L 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 7 " -0.014 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C SER L 7 " 0.046 2.00e-02 2.50e+03 pdb=" O SER L 7 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO L 8 " -0.015 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1070 2.83 - 3.35: 2861 3.35 - 3.86: 5945 3.86 - 4.38: 7279 4.38 - 4.90: 12391 Nonbonded interactions: 29546 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.532 3.120 nonbonded pdb=" N ASP H 54 " pdb=" N GLY H 55 " model vdw 2.566 2.560 nonbonded pdb=" OD1 ASN A 165 " pdb=" O5 NAG A1304 " model vdw 2.597 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" N THR A 109 " model vdw 2.610 3.120 ... (remaining 29541 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: 11.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.011 0.061 3700 Z= 0.598 Angle : 1.241 8.102 5034 Z= 0.831 Chirality : 0.074 0.317 561 Planarity : 0.006 0.029 631 Dihedral : 10.639 82.143 1379 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.04 (0.40), residues: 431 helix: -1.13 (1.30), residues: 17 sheet: 1.05 (0.35), residues: 206 loop : 0.62 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 67 TYR 0.028 0.004 TYR H 104 PHE 0.015 0.003 PHE A 55 TRP 0.020 0.005 TRP A 64 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01091 ( 3691) covalent geometry : angle 1.23173 ( 5011) SS BOND : bond 0.00707 ( 4) SS BOND : angle 3.04044 ( 8) hydrogen bonds : bond 0.13583 ( 143) hydrogen bonds : angle 8.17851 ( 369) link_NAG-ASN : bond 0.05832 ( 5) link_NAG-ASN : angle 2.17403 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.179 Fit side-chains REVERT: L 30 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8046 (mtm180) REVERT: L 81 GLU cc_start: 0.7524 (pm20) cc_final: 0.7197 (pm20) REVERT: H 34 MET cc_start: 0.9008 (mmm) cc_final: 0.8508 (mmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.4923 time to fit residues: 40.8054 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095331 restraints weight = 4251.064| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.38 r_work: 0.2844 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3700 Z= 0.134 Angle : 0.579 7.034 5034 Z= 0.295 Chirality : 0.045 0.167 561 Planarity : 0.004 0.033 631 Dihedral : 4.777 34.683 588 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.80 % Allowed : 9.02 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.43 (0.41), residues: 431 helix: 3.32 (1.70), residues: 11 sheet: 1.25 (0.35), residues: 203 loop : 0.64 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.011 0.001 TYR A 170 PHE 0.012 0.002 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3691) covalent geometry : angle 0.55316 ( 5011) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.87646 ( 8) hydrogen bonds : bond 0.03277 ( 143) hydrogen bonds : angle 5.89220 ( 369) link_NAG-ASN : bond 0.00761 ( 5) link_NAG-ASN : angle 3.15186 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.137 Fit side-chains REVERT: L 30 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.7910 (mtm180) REVERT: L 81 GLU cc_start: 0.8043 (pm20) cc_final: 0.7559 (pm20) REVERT: H 17 SER cc_start: 0.8924 (p) cc_final: 0.8661 (m) REVERT: H 89 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 129 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8504 (mtmt) REVERT: A 190 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8200 (mtm110) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.5493 time to fit residues: 35.6947 Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.092140 restraints weight = 4237.998| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.38 r_work: 0.2769 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3700 Z= 0.194 Angle : 0.604 9.261 5034 Z= 0.302 Chirality : 0.047 0.204 561 Planarity : 0.004 0.033 631 Dihedral : 5.619 49.244 588 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.35 % Allowed : 8.25 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.25 (0.41), residues: 431 helix: 0.44 (1.55), residues: 17 sheet: 1.30 (0.35), residues: 207 loop : 0.47 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.013 0.001 TYR A 279 PHE 0.012 0.002 PHE A 133 TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 3691) covalent geometry : angle 0.59336 ( 5011) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.82675 ( 8) hydrogen bonds : bond 0.03290 ( 143) hydrogen bonds : angle 5.71311 ( 369) link_NAG-ASN : bond 0.00595 ( 5) link_NAG-ASN : angle 2.12827 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.131 Fit side-chains REVERT: L 30 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.7878 (mtm180) REVERT: L 103 LYS cc_start: 0.8702 (tttt) cc_final: 0.8257 (tttp) REVERT: H 17 SER cc_start: 0.8909 (p) cc_final: 0.8679 (m) REVERT: H 89 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 129 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8484 (mtmt) REVERT: A 190 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8084 (mtt90) REVERT: A 287 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8514 (t0) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.5806 time to fit residues: 37.6599 Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.101106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.082818 restraints weight = 4403.589| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.60 r_work: 0.2661 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 3700 Z= 0.277 Angle : 0.673 10.454 5034 Z= 0.327 Chirality : 0.050 0.183 561 Planarity : 0.004 0.036 631 Dihedral : 6.093 48.694 588 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.35 % Allowed : 9.54 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.21 (0.40), residues: 431 helix: 3.57 (1.80), residues: 11 sheet: 1.36 (0.36), residues: 198 loop : 0.20 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.013 0.002 TYR A 279 PHE 0.015 0.002 PHE A 133 TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 3691) covalent geometry : angle 0.65168 ( 5011) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.04453 ( 8) hydrogen bonds : bond 0.03492 ( 143) hydrogen bonds : angle 5.80595 ( 369) link_NAG-ASN : bond 0.00371 ( 5) link_NAG-ASN : angle 3.07952 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.133 Fit side-chains REVERT: L 30 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.7872 (mtm180) REVERT: H 17 SER cc_start: 0.8905 (p) cc_final: 0.8683 (m) REVERT: H 89 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: A 129 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8474 (mtmt) REVERT: A 190 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8157 (mtm110) outliers start: 13 outliers final: 6 residues processed: 60 average time/residue: 0.5570 time to fit residues: 34.4443 Evaluate side-chains 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091881 restraints weight = 4273.387| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.45 r_work: 0.2780 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3700 Z= 0.122 Angle : 0.550 9.508 5034 Z= 0.270 Chirality : 0.044 0.148 561 Planarity : 0.004 0.034 631 Dihedral : 5.441 49.463 588 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 11.34 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.28 (0.41), residues: 431 helix: 3.33 (1.74), residues: 11 sheet: 1.43 (0.36), residues: 203 loop : 0.20 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR A 170 PHE 0.009 0.001 PHE A 133 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3691) covalent geometry : angle 0.52513 ( 5011) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.60639 ( 8) hydrogen bonds : bond 0.02735 ( 143) hydrogen bonds : angle 5.34302 ( 369) link_NAG-ASN : bond 0.00579 ( 5) link_NAG-ASN : angle 3.00578 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.113 Fit side-chains REVERT: L 30 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.7859 (mtm180) REVERT: L 42 LYS cc_start: 0.8836 (mptt) cc_final: 0.8345 (mmtm) REVERT: L 93 ASN cc_start: 0.8728 (p0) cc_final: 0.8527 (p0) REVERT: H 17 SER cc_start: 0.8875 (p) cc_final: 0.8652 (m) REVERT: H 89 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 129 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8477 (mtmt) REVERT: A 190 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8158 (mtm110) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.5669 time to fit residues: 37.9522 Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.101285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.082991 restraints weight = 4401.348| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.61 r_work: 0.2670 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3700 Z= 0.242 Angle : 0.642 9.495 5034 Z= 0.312 Chirality : 0.047 0.140 561 Planarity : 0.004 0.035 631 Dihedral : 5.836 45.813 588 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.58 % Allowed : 11.34 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.15 (0.41), residues: 431 helix: 3.50 (1.78), residues: 11 sheet: 1.36 (0.37), residues: 198 loop : 0.10 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 190 TYR 0.012 0.002 TYR H 95 PHE 0.014 0.002 PHE A 133 TRP 0.018 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 3691) covalent geometry : angle 0.61134 ( 5011) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.90082 ( 8) hydrogen bonds : bond 0.03259 ( 143) hydrogen bonds : angle 5.59452 ( 369) link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 3.58715 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.156 Fit side-chains REVERT: L 30 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.7844 (mtm180) REVERT: L 93 ASN cc_start: 0.8741 (p0) cc_final: 0.8538 (p0) REVERT: H 17 SER cc_start: 0.8890 (p) cc_final: 0.8659 (m) REVERT: H 89 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 129 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8467 (mtmt) REVERT: A 190 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8152 (mtm110) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.5545 time to fit residues: 34.3556 Evaluate side-chains 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.0060 chunk 42 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 2 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 overall best weight: 0.0750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.093352 restraints weight = 4323.133| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.45 r_work: 0.2822 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3700 Z= 0.090 Angle : 0.530 10.745 5034 Z= 0.259 Chirality : 0.044 0.159 561 Planarity : 0.004 0.034 631 Dihedral : 5.388 53.705 588 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.84 % Allowed : 12.37 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.29 (0.42), residues: 431 helix: 3.16 (1.72), residues: 11 sheet: 1.45 (0.37), residues: 204 loop : 0.20 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.011 0.001 TYR A 170 PHE 0.009 0.001 PHE A 133 TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 3691) covalent geometry : angle 0.49887 ( 5011) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.54174 ( 8) hydrogen bonds : bond 0.02453 ( 143) hydrogen bonds : angle 5.07672 ( 369) link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 3.33743 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.099 Fit side-chains REVERT: L 30 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.7843 (mtm180) REVERT: L 42 LYS cc_start: 0.8832 (mptt) cc_final: 0.8350 (mmtm) REVERT: L 70 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: A 129 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8435 (mtmt) REVERT: A 164 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.6897 (m-40) REVERT: A 190 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8122 (mtm110) outliers start: 11 outliers final: 4 residues processed: 68 average time/residue: 0.5880 time to fit residues: 41.1561 Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.090460 restraints weight = 4302.647| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.47 r_work: 0.2761 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3700 Z= 0.163 Angle : 0.580 9.121 5034 Z= 0.284 Chirality : 0.045 0.139 561 Planarity : 0.004 0.035 631 Dihedral : 5.506 45.351 588 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 13.14 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.24 (0.42), residues: 431 helix: 3.41 (1.77), residues: 11 sheet: 1.49 (0.39), residues: 190 loop : 0.15 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.012 0.001 TYR H 95 PHE 0.012 0.001 PHE A 133 TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3691) covalent geometry : angle 0.55100 ( 5011) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.64896 ( 8) hydrogen bonds : bond 0.02804 ( 143) hydrogen bonds : angle 5.27143 ( 369) link_NAG-ASN : bond 0.00126 ( 5) link_NAG-ASN : angle 3.32634 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.115 Fit side-chains REVERT: L 30 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.7838 (mtm180) REVERT: L 42 LYS cc_start: 0.8893 (mptt) cc_final: 0.8417 (mmtm) REVERT: H 13 GLN cc_start: 0.8502 (mm110) cc_final: 0.8265 (mm110) REVERT: H 114 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: A 129 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8471 (mtmt) REVERT: A 190 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8074 (mtm110) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.6007 time to fit residues: 36.4520 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 16 optimal weight: 0.0470 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.0470 overall best weight: 0.0874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.094733 restraints weight = 4234.283| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.46 r_work: 0.2836 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3700 Z= 0.088 Angle : 0.530 10.565 5034 Z= 0.260 Chirality : 0.044 0.141 561 Planarity : 0.004 0.035 631 Dihedral : 5.235 47.838 588 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.06 % Allowed : 13.14 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.19 (0.42), residues: 431 helix: 2.95 (1.68), residues: 11 sheet: 1.42 (0.37), residues: 198 loop : 0.15 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.010 0.001 TYR H 95 PHE 0.012 0.001 PHE A 133 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 3691) covalent geometry : angle 0.48349 ( 5011) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.84070 ( 8) hydrogen bonds : bond 0.02335 ( 143) hydrogen bonds : angle 4.98658 ( 369) link_NAG-ASN : bond 0.00183 ( 5) link_NAG-ASN : angle 3.98119 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.161 Fit side-chains REVERT: L 30 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.7793 (mtm180) REVERT: L 42 LYS cc_start: 0.8809 (mptt) cc_final: 0.8364 (mmtm) REVERT: H 13 GLN cc_start: 0.8504 (mm110) cc_final: 0.8107 (mp10) REVERT: H 114 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: A 167 THR cc_start: 0.8378 (p) cc_final: 0.8170 (t) REVERT: A 190 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8122 (mtm110) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.5743 time to fit residues: 37.2744 Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 0.0970 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.090924 restraints weight = 4302.587| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.50 r_work: 0.2765 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3700 Z= 0.159 Angle : 0.578 7.662 5034 Z= 0.285 Chirality : 0.046 0.140 561 Planarity : 0.004 0.035 631 Dihedral : 5.204 43.918 588 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 13.14 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.22 (0.42), residues: 431 helix: 3.40 (1.76), residues: 11 sheet: 1.50 (0.39), residues: 190 loop : 0.12 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.012 0.001 TYR H 95 PHE 0.013 0.001 PHE A 133 TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3691) covalent geometry : angle 0.55189 ( 5011) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.83131 ( 8) hydrogen bonds : bond 0.02792 ( 143) hydrogen bonds : angle 5.21912 ( 369) link_NAG-ASN : bond 0.00104 ( 5) link_NAG-ASN : angle 3.13537 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.132 Fit side-chains REVERT: L 30 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.7845 (mtm180) REVERT: L 42 LYS cc_start: 0.8883 (mptt) cc_final: 0.8379 (mmtm) REVERT: L 93 ASN cc_start: 0.8683 (p0) cc_final: 0.8400 (p0) REVERT: H 114 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: A 190 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8100 (mtm110) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.5791 time to fit residues: 34.6090 Evaluate side-chains 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.092340 restraints weight = 4211.594| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.47 r_work: 0.2801 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3700 Z= 0.126 Angle : 0.532 6.950 5034 Z= 0.267 Chirality : 0.044 0.133 561 Planarity : 0.004 0.035 631 Dihedral : 4.818 39.642 588 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.80 % Allowed : 13.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: 1.16 (0.42), residues: 431 helix: 3.12 (1.70), residues: 11 sheet: 1.45 (0.38), residues: 195 loop : 0.07 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.011 0.001 TYR H 95 PHE 0.011 0.001 PHE A 133 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3691) covalent geometry : angle 0.51424 ( 5011) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.77152 ( 8) hydrogen bonds : bond 0.02572 ( 143) hydrogen bonds : angle 5.06612 ( 369) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 2.54374 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.63 seconds wall clock time: 27 minutes 3.03 seconds (1623.03 seconds total)