Starting phenix.real_space_refine on Wed Jul 1 22:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8i_24237/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8i_24237/07_2026/7n8i_24237.cif" } 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-6108/lib/python3.11/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 chiralities: 5 Time building chain proxies: 1.00, per 1000 atoms: 0.28 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: 0.31 Conformation dependent library (CDL) restraints added in 110.8 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: 0.07 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: 0.34 Time building geometry restraints manager: 0.40 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: 2013 16.43 - 32.86: 72 32.86 - 49.29: 13 49.29 - 65.72: 10 65.72 - 82.14: 4 Dihedral angle restraints: 2112 sinusoidal: 820 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 2109 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: 9.580 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.620 Find NCS groups from input model: 0.020 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 : 10.877 82.143 1274 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/Z covalent geometry : bond 0.01091 / 0.59 ( 3691) covalent geometry : angle 1.23173 / 0.83 ( 5011) SS BOND : bond 0.00707 / 0.34 ( 4) SS BOND : angle 3.04044 / 1.69 ( 8) hydrogen bonds : bond 0.13583 / 9.47 ( 143) hydrogen bonds : angle 8.17851 / 5.78 ( 369) link_NAG-ASN : bond 0.05832 / 3.09 ( 5) link_NAG-ASN : angle 2.17403 / 1.26 ( 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 : 0.131 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: 0.4686 time to fit residues: 38.8373 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 : 0.131 ------------------------------------------------------------------------------- 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... 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 = 0.3173 r_free = 0.3173 target = 0.111486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095297 restraints weight = 4231.490| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.39 r_work: 0.2845 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3700 Z= 0.133 Angle : 0.579 7.368 5034 Z= 0.293 Chirality : 0.045 0.165 561 Planarity : 0.004 0.033 631 Dihedral : 4.500 16.428 483 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 1.42 (0.41), residues: 431 helix: 3.30 (1.70), residues: 11 sheet: 1.25 (0.35), residues: 203 loop : 0.63 (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 0.011 0.002 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 3691) covalent geometry : angle 0.55235 / 0.29 ( 5011) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 0.82173 / 0.44 ( 8) hydrogen bonds : bond 0.03129 / 2.08 ( 143) hydrogen bonds : angle 5.84064 / 4.21 ( 369) link_NAG-ASN : bond 0.00635 / 0.24 ( 5) link_NAG-ASN : angle 3.18251 / 1.73 ( 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 : 0.140 Fit side-chains REVERT: L 30 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.7905 (mtm180) REVERT: L 81 GLU cc_start: 0.8056 (pm20) cc_final: 0.7568 (pm20) REVERT: H 17 SER cc_start: 0.8926 (p) cc_final: 0.8660 (m) REVERT: H 89 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: A 129 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8516 (mtmt) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.5514 time to fit residues: 35.8401 Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 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 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 overall best weight: 0.2458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.096021 restraints weight = 4213.558| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.31 r_work: 0.2821 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3700 Z= 0.139 Angle : 0.558 7.255 5034 Z= 0.282 Chirality : 0.046 0.220 561 Planarity : 0.004 0.032 631 Dihedral : 4.411 16.682 483 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 8.76 % Favored : 88.66 % 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: 0.30 (1.51), residues: 17 sheet: 1.32 (0.35), residues: 210 loop : 0.50 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.011 0.001 TYR H 95 PHE 0.009 0.001 PHE A 133 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3691) covalent geometry : angle 0.54761 / 0.28 ( 5011) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 0.70306 / 0.36 ( 8) hydrogen bonds : bond 0.03011 / 2.02 ( 143) hydrogen bonds : angle 5.55728 / 4.00 ( 369) link_NAG-ASN : bond 0.00657 / 0.25 ( 5) link_NAG-ASN : angle 1.99652 / 1.05 ( 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 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.136 Fit side-chains REVERT: L 30 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8021 (mtm180) REVERT: L 42 LYS cc_start: 0.8853 (mptt) cc_final: 0.8457 (mmtm) REVERT: H 17 SER cc_start: 0.8960 (p) cc_final: 0.8713 (m) REVERT: H 89 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 41 LYS cc_start: 0.7057 (mmpt) cc_final: 0.4980 (tmtt) REVERT: A 129 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8550 (mtmt) REVERT: A 205 SER cc_start: 0.9110 (p) cc_final: 0.8887 (t) REVERT: A 287 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8503 (t0) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.5142 time to fit residues: 33.3897 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 : 0.159 ------------------------------------------------------------------------------- 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 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 57 ASN A 115 GLN A 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.102488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.083884 restraints weight = 4379.119| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.62 r_work: 0.2696 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 3700 Z= 0.222 Angle : 0.638 12.245 5034 Z= 0.308 Chirality : 0.050 0.412 561 Planarity : 0.004 0.034 631 Dihedral : 4.703 17.616 483 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.09 % Allowed : 9.54 % Favored : 87.37 % 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: 1.41 (0.41), residues: 431 helix: 3.54 (1.79), residues: 11 sheet: 1.52 (0.36), residues: 198 loop : 0.31 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 72 TYR 0.013 0.002 TYR A 279 PHE 0.014 0.002 PHE A 133 TRP 0.017 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.22 ( 3691) covalent geometry : angle 0.63217 / 0.31 ( 5011) SS BOND : bond 0.00336 / 0.17 ( 4) SS BOND : angle 0.86544 / 0.46 ( 8) hydrogen bonds : bond 0.03237 / 2.17 ( 143) hydrogen bonds : angle 5.68425 / 4.07 ( 369) link_NAG-ASN : bond 0.00599 / 0.24 ( 5) link_NAG-ASN : angle 1.63152 / 0.89 ( 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 70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.137 Fit side-chains REVERT: L 30 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.7841 (mtm180) REVERT: L 103 LYS cc_start: 0.8735 (tttt) cc_final: 0.8145 (tptp) REVERT: H 17 SER cc_start: 0.8885 (p) cc_final: 0.8661 (m) REVERT: H 89 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 102 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: A 129 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8472 (mtmt) REVERT: A 205 SER cc_start: 0.9197 (p) cc_final: 0.8942 (t) REVERT: A 287 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8456 (t0) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.5662 time to fit residues: 36.7484 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 : 0.159 ------------------------------------------------------------------------------- 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 102 ARG Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.103344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.084681 restraints weight = 4375.567| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.63 r_work: 0.2696 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3700 Z= 0.184 Angle : 0.617 10.909 5034 Z= 0.296 Chirality : 0.047 0.219 561 Planarity : 0.004 0.035 631 Dihedral : 4.590 17.054 483 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.84 % Allowed : 10.31 % Favored : 86.86 % 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: 1.35 (0.41), residues: 431 helix: 3.51 (1.77), residues: 11 sheet: 1.53 (0.36), residues: 198 loop : 0.21 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR H 95 PHE 0.012 0.002 PHE A 133 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.18 ( 3691) covalent geometry : angle 0.58743 / 0.29 ( 5011) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.75982 / 0.41 ( 8) hydrogen bonds : bond 0.03056 / 2.05 ( 143) hydrogen bonds : angle 5.49792 / 3.94 ( 369) link_NAG-ASN : bond 0.00175 / 0.09 ( 5) link_NAG-ASN : angle 3.46522 / 1.88 ( 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 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.133 Fit side-chains REVERT: L 30 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.7862 (mtm180) REVERT: L 42 LYS cc_start: 0.8840 (mptt) cc_final: 0.8499 (mmtp) REVERT: L 93 ASN cc_start: 0.8767 (p0) cc_final: 0.8566 (p0) REVERT: L 103 LYS cc_start: 0.8725 (tttt) cc_final: 0.8250 (tttp) REVERT: H 17 SER cc_start: 0.8882 (p) cc_final: 0.8660 (m) REVERT: H 89 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: A 102 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7763 (mtp85) REVERT: A 129 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8480 (mtmt) REVERT: A 205 SER cc_start: 0.9155 (p) cc_final: 0.8950 (t) outliers start: 11 outliers final: 4 residues processed: 63 average time/residue: 0.6036 time to fit residues: 39.2291 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 : 0.141 ------------------------------------------------------------------------------- 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 102 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 28 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.103366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.085022 restraints weight = 4361.088| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.59 r_work: 0.2725 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3700 Z= 0.175 Angle : 0.578 9.124 5034 Z= 0.284 Chirality : 0.050 0.438 561 Planarity : 0.004 0.035 631 Dihedral : 4.552 16.678 483 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 10.82 % Favored : 86.60 % 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 (0.41), residues: 431 helix: 3.54 (1.78), residues: 11 sheet: 1.53 (0.37), residues: 198 loop : 0.13 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR H 95 PHE 0.013 0.002 PHE A 133 TRP 0.016 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 3691) covalent geometry : angle 0.57419 / 0.28 ( 5011) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 0.78893 / 0.41 ( 8) hydrogen bonds : bond 0.02936 / 1.97 ( 143) hydrogen bonds : angle 5.42108 / 3.88 ( 369) link_NAG-ASN : bond 0.00184 / 0.09 ( 5) link_NAG-ASN : angle 1.28356 / 0.69 ( 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 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.132 Fit side-chains REVERT: L 30 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.7846 (mtm180) REVERT: L 103 LYS cc_start: 0.8735 (tttt) cc_final: 0.8261 (tttp) REVERT: H 17 SER cc_start: 0.8866 (p) cc_final: 0.8657 (m) REVERT: H 89 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: A 102 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7770 (mtp85) REVERT: A 129 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8476 (mtmt) REVERT: A 190 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8101 (mtm110) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.5118 time to fit residues: 32.7133 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 : 0.131 ------------------------------------------------------------------------------- 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 102 ARG Chi-restraints excluded: chain A residue 112 SER 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: 0.9990 chunk 36 optimal weight: 0.0670 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.084673 restraints weight = 4441.917| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.61 r_work: 0.2712 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3700 Z= 0.186 Angle : 0.572 7.837 5034 Z= 0.287 Chirality : 0.049 0.312 561 Planarity : 0.004 0.035 631 Dihedral : 4.608 16.714 483 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 10.57 % Favored : 86.60 % 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 (0.41), residues: 431 helix: 3.58 (1.78), residues: 11 sheet: 1.49 (0.38), residues: 189 loop : 0.08 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR H 95 PHE 0.013 0.002 PHE A 133 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 3691) covalent geometry : angle 0.56640 / 0.29 ( 5011) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.87411 / 0.43 ( 8) hydrogen bonds : bond 0.02975 / 1.99 ( 143) hydrogen bonds : angle 5.44574 / 3.89 ( 369) link_NAG-ASN : bond 0.00155 / 0.08 ( 5) link_NAG-ASN : angle 1.54883 / 0.79 ( 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 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.205 Fit side-chains REVERT: L 30 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.7838 (mtm180) REVERT: L 42 LYS cc_start: 0.8884 (mptt) cc_final: 0.8349 (mmtm) REVERT: H 17 SER cc_start: 0.8875 (p) cc_final: 0.8669 (m) REVERT: H 89 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: A 129 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8474 (mtmt) REVERT: A 190 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8121 (mtm110) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.6007 time to fit residues: 38.9402 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- 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: 0.1980 chunk 25 optimal weight: 0.0010 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 36 optimal weight: 0.0270 overall best weight: 0.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.101906 restraints weight = 4152.940| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.31 r_work: 0.2865 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3700 Z= 0.087 Angle : 0.494 6.331 5034 Z= 0.248 Chirality : 0.046 0.299 561 Planarity : 0.004 0.035 631 Dihedral : 4.183 14.796 483 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.80 % Allowed : 11.34 % Favored : 86.86 % 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: 1.26 (0.43), residues: 431 helix: 3.10 (1.69), residues: 11 sheet: 1.43 (0.36), residues: 207 loop : 0.16 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.011 0.001 TYR A 170 PHE 0.012 0.001 PHE A 133 TRP 0.011 0.001 TRP A 64 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 3691) covalent geometry : angle 0.48602 / 0.25 ( 5011) SS BOND : bond 0.00227 / 0.11 ( 4) SS BOND : angle 0.67767 / 0.29 ( 8) hydrogen bonds : bond 0.02342 / 1.58 ( 143) hydrogen bonds : angle 4.97368 / 3.56 ( 369) link_NAG-ASN : bond 0.00309 / 0.12 ( 5) link_NAG-ASN : angle 1.70461 / 0.82 ( 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 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.147 Fit side-chains REVERT: L 30 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.7921 (mtm180) REVERT: L 42 LYS cc_start: 0.8819 (mptt) cc_final: 0.8426 (mmtm) REVERT: L 103 LYS cc_start: 0.8686 (tttt) cc_final: 0.8181 (tttp) REVERT: H 17 SER cc_start: 0.8840 (p) cc_final: 0.8636 (m) REVERT: A 129 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8439 (mtmt) REVERT: A 167 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8152 (t) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.5395 time to fit residues: 36.2114 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3023 r_free = 0.3023 target = 0.103363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.084587 restraints weight = 4339.143| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.62 r_work: 0.2699 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3700 Z= 0.229 Angle : 0.640 7.851 5034 Z= 0.313 Chirality : 0.053 0.421 561 Planarity : 0.004 0.036 631 Dihedral : 4.717 16.417 483 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.06 % Allowed : 12.63 % 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: 1.15 (0.42), residues: 431 helix: 3.61 (1.80), residues: 11 sheet: 1.43 (0.39), residues: 190 loop : 0.08 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 72 TYR 0.014 0.002 TYR A 160 PHE 0.017 0.002 PHE A 133 TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 ( 3691) covalent geometry : angle 0.62572 / 0.31 ( 5011) SS BOND : bond 0.00344 / 0.16 ( 4) SS BOND : angle 0.90812 / 0.45 ( 8) hydrogen bonds : bond 0.03170 / 2.14 ( 143) hydrogen bonds : angle 5.47677 / 3.88 ( 369) link_NAG-ASN : bond 0.00372 / 0.15 ( 5) link_NAG-ASN : angle 2.46551 / 1.11 ( 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 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.166 Fit side-chains REVERT: L 30 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.7871 (mtm180) REVERT: H 13 GLN cc_start: 0.8516 (mm110) cc_final: 0.8267 (mm110) REVERT: H 17 SER cc_start: 0.8891 (p) cc_final: 0.8669 (m) REVERT: H 114 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7420 (pm20) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.5364 time to fit residues: 32.2061 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 0.0770 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3173 r_free = 0.3173 target = 0.112007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.095405 restraints weight = 4260.813| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.43 r_work: 0.2843 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3700 Z= 0.094 Angle : 0.530 6.745 5034 Z= 0.263 Chirality : 0.048 0.332 561 Planarity : 0.004 0.034 631 Dihedral : 4.224 15.261 483 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.55 % Allowed : 13.92 % 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: 1.10 (0.43), residues: 431 helix: 3.07 (1.71), residues: 11 sheet: 1.36 (0.37), residues: 199 loop : 0.05 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.010 0.001 TYR H 95 PHE 0.016 0.001 PHE A 133 TRP 0.012 0.001 TRP A 64 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 3691) covalent geometry : angle 0.51522 / 0.26 ( 5011) SS BOND : bond 0.00256 / 0.11 ( 4) SS BOND : angle 0.86407 / 0.43 ( 8) hydrogen bonds : bond 0.02469 / 1.66 ( 143) hydrogen bonds : angle 4.98668 / 3.55 ( 369) link_NAG-ASN : bond 0.00360 / 0.14 ( 5) link_NAG-ASN : angle 2.26287 / 1.04 ( 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 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.100 Fit side-chains REVERT: L 30 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.7823 (mtm180) REVERT: L 42 LYS cc_start: 0.8827 (mptt) cc_final: 0.8469 (mmtm) REVERT: L 93 ASN cc_start: 0.8679 (p0) cc_final: 0.8378 (p0) REVERT: H 114 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7407 (pm20) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.5307 time to fit residues: 32.3834 Evaluate side-chains 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.093234 restraints weight = 4201.354| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.46 r_work: 0.2798 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3700 Z= 0.132 Angle : 0.561 7.371 5034 Z= 0.277 Chirality : 0.048 0.335 561 Planarity : 0.004 0.035 631 Dihedral : 4.351 15.425 483 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.80 % Allowed : 14.18 % Favored : 84.02 % 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: 1.20 (0.42), residues: 431 helix: 3.38 (1.75), residues: 11 sheet: 1.43 (0.38), residues: 195 loop : 0.13 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.012 0.001 TYR A 160 PHE 0.015 0.001 PHE A 133 TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 3691) covalent geometry : angle 0.54962 / 0.27 ( 5011) SS BOND : bond 0.00242 / 0.11 ( 4) SS BOND : angle 0.82061 / 0.40 ( 8) hydrogen bonds : bond 0.02711 / 1.83 ( 143) hydrogen bonds : angle 5.12198 / 3.64 ( 369) link_NAG-ASN : bond 0.00262 / 0.10 ( 5) link_NAG-ASN : angle 2.09970 / 0.99 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.19 seconds wall clock time: 27 minutes 40.76 seconds (1660.76 seconds total)