Starting phenix.real_space_refine on Tue Mar 3 12:22:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2026/8dm4_27526.map" } resolution = 2.45 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= -0.001 sd= 0.017 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 18 5.16 5 C 2563 2.51 5 N 653 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.98, per 1000 atoms: 0.24 Number of scatterers: 4018 At special positions: 0 Unit cell: (101, 61, 97, 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 18 16.00 O 784 8.00 N 653 7.00 C 2563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 142.2 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 1.6% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.905A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.766A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.711A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.284A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 0.58 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1249 1.34 - 1.46: 1064 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 4117 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 4112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5350 2.08 - 4.16: 220 4.16 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 5594 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C LEU A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 122.93 118.21 4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.47 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.29e+00 angle pdb=" N THR L 34 " pdb=" CA THR L 34 " pdb=" C THR L 34 " ideal model delta sigma weight residual 110.35 106.53 3.82 1.38e+00 5.25e-01 7.64e+00 ... (remaining 5589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2302 17.82 - 35.63: 148 35.63 - 53.45: 27 53.45 - 71.27: 13 71.27 - 89.09: 4 Dihedral angle restraints: 2494 sinusoidal: 1051 harmonic: 1443 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -51.05 -34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA VAL H 24 " pdb=" C VAL H 24 " pdb=" N GLU H 25 " pdb=" CA GLU H 25 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 424 0.051 - 0.102: 159 0.102 - 0.152: 44 0.152 - 0.203: 4 0.203 - 0.254: 3 Chirality restraints: 634 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 631 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 27 " -0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 28 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 28 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.237 9.50e-02 1.11e+02 1.07e-01 7.74e+00 pdb=" NE ARG A 273 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C ILE A 210 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 865 2.79 - 3.32: 3144 3.32 - 3.84: 6623 3.84 - 4.37: 7758 4.37 - 4.90: 13925 Nonbonded interactions: 32315 Sorted by model distance: nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.279 3.040 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.307 3.040 nonbonded pdb=" OG SER A 247 " pdb=" OH TYR H 46 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.368 3.040 ... (remaining 32310 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: 6.130 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.006 0.045 4127 Z= 0.271 Angle : 0.925 10.390 5620 Z= 0.489 Chirality : 0.057 0.254 634 Planarity : 0.008 0.107 706 Dihedral : 13.358 89.087 1558 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.55 (0.34), residues: 230 loop : -0.55 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 273 TYR 0.032 0.003 TYR A 145 PHE 0.025 0.003 PHE A 175 TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 4117) covalent geometry : angle 0.90354 ( 5594) SS BOND : bond 0.00341 ( 4) SS BOND : angle 2.19227 ( 8) hydrogen bonds : bond 0.07968 ( 153) hydrogen bonds : angle 6.59570 ( 399) link_BETA1-4 : bond 0.01012 ( 1) link_BETA1-4 : angle 2.50579 ( 3) link_NAG-ASN : bond 0.00372 ( 5) link_NAG-ASN : angle 3.54620 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.154 Fit side-chains REVERT: A 80 ASP cc_start: 0.6299 (t0) cc_final: 0.6086 (t0) REVERT: A 100 ILE cc_start: 0.8408 (mp) cc_final: 0.8064 (tp) REVERT: H 52 SER cc_start: 0.7982 (m) cc_final: 0.7705 (p) REVERT: H 65 GLU cc_start: 0.6701 (pt0) cc_final: 0.6168 (pm20) REVERT: H 107 SER cc_start: 0.7089 (m) cc_final: 0.6425 (t) REVERT: H 131 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: H 134 MET cc_start: 0.8612 (mtm) cc_final: 0.8405 (mpp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.5368 time to fit residues: 55.4782 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 30 ASN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.145334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101539 restraints weight = 5702.189| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.21 r_work: 0.3226 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4127 Z= 0.134 Angle : 0.606 8.441 5620 Z= 0.311 Chirality : 0.045 0.210 634 Planarity : 0.004 0.055 706 Dihedral : 7.397 58.172 665 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 10.30 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.31 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.79 (0.35), residues: 215 loop : -0.23 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.013 0.001 TYR A 28 PHE 0.014 0.001 PHE A 175 TRP 0.014 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4117) covalent geometry : angle 0.58528 ( 5594) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.44985 ( 8) hydrogen bonds : bond 0.03742 ( 153) hydrogen bonds : angle 5.98668 ( 399) link_BETA1-4 : bond 0.00106 ( 1) link_BETA1-4 : angle 1.48767 ( 3) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 2.90108 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.123 Fit side-chains REVERT: A 80 ASP cc_start: 0.6506 (t0) cc_final: 0.6049 (t0) REVERT: A 115 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8176 (mm110) REVERT: A 169 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 173 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: A 281 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: H 65 GLU cc_start: 0.7345 (pt0) cc_final: 0.6697 (pm20) REVERT: H 100 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6494 (ttp) REVERT: H 109 ASP cc_start: 0.7099 (t0) cc_final: 0.6848 (t0) REVERT: H 131 TYR cc_start: 0.8127 (t80) cc_final: 0.7881 (t80) REVERT: H 134 MET cc_start: 0.8742 (mtm) cc_final: 0.8452 (mpp) REVERT: L 132 LYS cc_start: 0.7576 (mmmm) cc_final: 0.7367 (mmmm) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.6600 time to fit residues: 48.1861 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098541 restraints weight = 5638.694| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.20 r_work: 0.3179 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4127 Z= 0.202 Angle : 0.629 6.314 5620 Z= 0.324 Chirality : 0.046 0.210 634 Planarity : 0.004 0.048 706 Dihedral : 6.965 55.600 665 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 11.90 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.79 (0.35), residues: 215 loop : -0.17 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.015 0.002 TYR A 28 PHE 0.025 0.002 PHE A 175 TRP 0.013 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 4117) covalent geometry : angle 0.60691 ( 5594) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.55196 ( 8) hydrogen bonds : bond 0.03914 ( 153) hydrogen bonds : angle 5.98709 ( 399) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 1.16212 ( 3) link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 3.08688 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.160 Fit side-chains REVERT: A 14 GLN cc_start: 0.7702 (mt0) cc_final: 0.7462 (mt0) REVERT: A 80 ASP cc_start: 0.6678 (t0) cc_final: 0.6231 (t0) REVERT: A 115 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8209 (mm110) REVERT: A 137 ASN cc_start: 0.8469 (m110) cc_final: 0.7990 (t0) REVERT: A 169 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: A 173 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: A 177 MET cc_start: 0.7951 (pmt) cc_final: 0.7656 (pmt) REVERT: H 65 GLU cc_start: 0.7472 (pt0) cc_final: 0.7136 (pt0) REVERT: H 78 MET cc_start: 0.7098 (tpp) cc_final: 0.6191 (tpt) REVERT: H 100 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7188 (tmt) REVERT: H 109 ASP cc_start: 0.7401 (t0) cc_final: 0.7137 (t0) REVERT: H 131 TYR cc_start: 0.8217 (t80) cc_final: 0.7867 (t80) REVERT: H 134 MET cc_start: 0.8788 (mtm) cc_final: 0.8480 (mpp) REVERT: L 98 LEU cc_start: 0.6914 (tp) cc_final: 0.6710 (tp) REVERT: L 117 THR cc_start: 0.8452 (p) cc_final: 0.8209 (p) REVERT: L 132 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7362 (mmmm) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.5778 time to fit residues: 43.4845 Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098618 restraints weight = 5588.087| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.22 r_work: 0.3187 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4127 Z= 0.179 Angle : 0.613 6.170 5620 Z= 0.315 Chirality : 0.045 0.201 634 Planarity : 0.004 0.043 706 Dihedral : 6.533 51.534 665 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.75 % Allowed : 13.27 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.43 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.84 (0.35), residues: 212 loop : -0.10 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 273 TYR 0.014 0.002 TYR A 28 PHE 0.021 0.002 PHE A 175 TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4117) covalent geometry : angle 0.58985 ( 5594) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.92255 ( 8) hydrogen bonds : bond 0.03746 ( 153) hydrogen bonds : angle 5.89082 ( 399) link_BETA1-4 : bond 0.00163 ( 1) link_BETA1-4 : angle 1.03338 ( 3) link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 2.98676 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.123 Fit side-chains REVERT: A 80 ASP cc_start: 0.6710 (t0) cc_final: 0.6254 (t0) REVERT: A 137 ASN cc_start: 0.8495 (m110) cc_final: 0.8025 (t0) REVERT: A 169 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: A 173 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: H 65 GLU cc_start: 0.7494 (pt0) cc_final: 0.7155 (pt0) REVERT: H 78 MET cc_start: 0.7028 (tpp) cc_final: 0.6089 (tpt) REVERT: H 100 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7135 (ttp) REVERT: H 134 MET cc_start: 0.8756 (mtm) cc_final: 0.8484 (mpp) REVERT: L 60 TRP cc_start: 0.8455 (m100) cc_final: 0.8246 (m100) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 0.5464 time to fit residues: 40.7602 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098887 restraints weight = 5598.345| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.19 r_work: 0.3192 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4127 Z= 0.169 Angle : 0.601 5.955 5620 Z= 0.312 Chirality : 0.045 0.197 634 Planarity : 0.004 0.041 706 Dihedral : 6.190 51.113 665 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 14.87 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.45 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.86 (0.35), residues: 212 loop : -0.10 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.013 0.002 TYR A 28 PHE 0.020 0.002 PHE A 175 TRP 0.012 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4117) covalent geometry : angle 0.57875 ( 5594) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.76846 ( 8) hydrogen bonds : bond 0.03659 ( 153) hydrogen bonds : angle 5.84285 ( 399) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 1.06785 ( 3) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 2.93756 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.141 Fit side-chains REVERT: A 14 GLN cc_start: 0.7844 (mt0) cc_final: 0.7369 (mt0) REVERT: A 80 ASP cc_start: 0.6697 (t0) cc_final: 0.6230 (t0) REVERT: A 137 ASN cc_start: 0.8491 (m110) cc_final: 0.8049 (t0) REVERT: A 169 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: A 173 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: H 65 GLU cc_start: 0.7519 (pt0) cc_final: 0.7154 (pt0) REVERT: H 78 MET cc_start: 0.7029 (tpp) cc_final: 0.6122 (tpt) REVERT: H 100 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7170 (tmm) REVERT: H 109 ASP cc_start: 0.7313 (t0) cc_final: 0.7090 (t0) REVERT: H 134 MET cc_start: 0.8736 (mtm) cc_final: 0.8534 (mpp) REVERT: H 135 ASP cc_start: 0.8271 (m-30) cc_final: 0.8014 (m-30) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.5621 time to fit residues: 41.1713 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS H 58 GLN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097210 restraints weight = 5590.046| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.22 r_work: 0.3162 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4127 Z= 0.217 Angle : 0.632 6.488 5620 Z= 0.327 Chirality : 0.047 0.200 634 Planarity : 0.004 0.041 706 Dihedral : 6.093 50.506 665 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 15.79 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.42 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.93 (0.36), residues: 206 loop : -0.18 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.015 0.002 TYR A 28 PHE 0.025 0.002 PHE A 175 TRP 0.015 0.002 TRP H 66 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 4117) covalent geometry : angle 0.60861 ( 5594) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.83744 ( 8) hydrogen bonds : bond 0.03876 ( 153) hydrogen bonds : angle 5.95049 ( 399) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 1.17017 ( 3) link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 3.05515 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.197 Fit side-chains REVERT: A 14 GLN cc_start: 0.7810 (mt0) cc_final: 0.7364 (mt0) REVERT: A 15 CYS cc_start: 0.8264 (m) cc_final: 0.8033 (m) REVERT: A 80 ASP cc_start: 0.6777 (t0) cc_final: 0.6327 (t0) REVERT: A 137 ASN cc_start: 0.8488 (m110) cc_final: 0.8037 (t0) REVERT: A 169 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: A 173 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: H 48 LEU cc_start: 0.7981 (tp) cc_final: 0.7775 (mt) REVERT: H 50 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8247 (mt-10) REVERT: H 58 GLN cc_start: 0.7267 (tt0) cc_final: 0.7031 (tt0) REVERT: H 65 GLU cc_start: 0.7486 (pt0) cc_final: 0.7063 (pt0) REVERT: H 78 MET cc_start: 0.6929 (tpp) cc_final: 0.6022 (tpt) REVERT: H 100 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7174 (ttp) REVERT: H 109 ASP cc_start: 0.7352 (t0) cc_final: 0.7125 (t0) REVERT: H 135 ASP cc_start: 0.8288 (m-30) cc_final: 0.7981 (m-30) REVERT: L 24 MET cc_start: 0.7019 (mmt) cc_final: 0.6428 (mmt) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.5628 time to fit residues: 44.1682 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.144216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101351 restraints weight = 5646.442| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.27 r_work: 0.3225 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4127 Z= 0.101 Angle : 0.552 5.025 5620 Z= 0.288 Chirality : 0.044 0.184 634 Planarity : 0.003 0.040 706 Dihedral : 5.521 52.011 665 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.60 % Allowed : 18.31 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.54 (0.39), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 220 loop : -0.02 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.010 0.001 TYR H 132 PHE 0.018 0.001 PHE H 70 TRP 0.009 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 4117) covalent geometry : angle 0.53231 ( 5594) SS BOND : bond 0.00679 ( 4) SS BOND : angle 1.56929 ( 8) hydrogen bonds : bond 0.03278 ( 153) hydrogen bonds : angle 5.63552 ( 399) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 1.19301 ( 3) link_NAG-ASN : bond 0.00140 ( 5) link_NAG-ASN : angle 2.62522 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.093 Fit side-chains REVERT: A 14 GLN cc_start: 0.7812 (mt0) cc_final: 0.7412 (mt0) REVERT: A 80 ASP cc_start: 0.6771 (t0) cc_final: 0.6282 (t0) REVERT: A 137 ASN cc_start: 0.8518 (m110) cc_final: 0.8071 (t0) REVERT: A 173 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: A 211 ASN cc_start: 0.8976 (p0) cc_final: 0.8742 (p0) REVERT: H 48 LEU cc_start: 0.7777 (tp) cc_final: 0.7569 (mt) REVERT: H 58 GLN cc_start: 0.7190 (tt0) cc_final: 0.6970 (tt0) REVERT: H 65 GLU cc_start: 0.7438 (pt0) cc_final: 0.6995 (pt0) REVERT: H 78 MET cc_start: 0.6945 (tpp) cc_final: 0.5996 (tpt) REVERT: H 100 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: H 109 ASP cc_start: 0.7200 (t0) cc_final: 0.6951 (t0) REVERT: H 135 ASP cc_start: 0.8331 (m-30) cc_final: 0.8021 (m-30) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.5820 time to fit residues: 42.7270 Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098200 restraints weight = 5472.294| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.25 r_work: 0.3173 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4127 Z= 0.189 Angle : 0.620 6.599 5620 Z= 0.319 Chirality : 0.046 0.199 634 Planarity : 0.004 0.040 706 Dihedral : 5.686 50.557 665 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.83 % Allowed : 19.22 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.46 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 214 loop : -0.12 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.014 0.001 TYR A 28 PHE 0.023 0.002 PHE A 175 TRP 0.014 0.002 TRP H 66 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4117) covalent geometry : angle 0.59865 ( 5594) SS BOND : bond 0.00323 ( 4) SS BOND : angle 1.75695 ( 8) hydrogen bonds : bond 0.03681 ( 153) hydrogen bonds : angle 5.76877 ( 399) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 1.22577 ( 3) link_NAG-ASN : bond 0.00300 ( 5) link_NAG-ASN : angle 2.92750 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.215 Fit side-chains REVERT: A 14 GLN cc_start: 0.7803 (mt0) cc_final: 0.7362 (mt0) REVERT: A 15 CYS cc_start: 0.8261 (m) cc_final: 0.8022 (m) REVERT: A 80 ASP cc_start: 0.6785 (t0) cc_final: 0.6330 (t0) REVERT: A 137 ASN cc_start: 0.8499 (m110) cc_final: 0.8039 (t0) REVERT: A 173 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: A 177 MET cc_start: 0.7936 (pmt) cc_final: 0.7653 (pmt) REVERT: A 211 ASN cc_start: 0.8993 (p0) cc_final: 0.8753 (p0) REVERT: H 58 GLN cc_start: 0.7192 (tt0) cc_final: 0.6950 (tt0) REVERT: H 65 GLU cc_start: 0.7425 (pt0) cc_final: 0.6995 (pt0) REVERT: H 100 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7140 (ttp) REVERT: H 109 ASP cc_start: 0.7269 (t0) cc_final: 0.7046 (t0) REVERT: H 135 ASP cc_start: 0.8269 (m-30) cc_final: 0.7974 (m-30) REVERT: L 132 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7511 (mmmm) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.5657 time to fit residues: 42.7370 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 0.0060 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.143522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100765 restraints weight = 5651.138| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.25 r_work: 0.3215 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4127 Z= 0.116 Angle : 0.572 5.732 5620 Z= 0.298 Chirality : 0.044 0.187 634 Planarity : 0.003 0.040 706 Dihedral : 5.456 51.857 665 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.60 % Allowed : 20.14 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.44 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.36), residues: 212 loop : -0.14 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.011 0.001 TYR H 132 PHE 0.019 0.001 PHE H 70 TRP 0.012 0.001 TRP L 60 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4117) covalent geometry : angle 0.55300 ( 5594) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.55974 ( 8) hydrogen bonds : bond 0.03311 ( 153) hydrogen bonds : angle 5.63333 ( 399) link_BETA1-4 : bond 0.00353 ( 1) link_BETA1-4 : angle 1.21007 ( 3) link_NAG-ASN : bond 0.00145 ( 5) link_NAG-ASN : angle 2.67193 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.159 Fit side-chains REVERT: A 14 GLN cc_start: 0.7768 (mt0) cc_final: 0.7348 (mt0) REVERT: A 15 CYS cc_start: 0.8206 (m) cc_final: 0.7965 (m) REVERT: A 80 ASP cc_start: 0.6781 (t0) cc_final: 0.6327 (t0) REVERT: A 137 ASN cc_start: 0.8503 (m110) cc_final: 0.8082 (t0) REVERT: A 177 MET cc_start: 0.8002 (pmt) cc_final: 0.7636 (pmt) REVERT: A 211 ASN cc_start: 0.8889 (p0) cc_final: 0.8650 (p0) REVERT: H 58 GLN cc_start: 0.7177 (tt0) cc_final: 0.6914 (tt0) REVERT: H 65 GLU cc_start: 0.7420 (pt0) cc_final: 0.7011 (pt0) REVERT: H 100 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7070 (ttp) REVERT: H 135 ASP cc_start: 0.8300 (m-30) cc_final: 0.8010 (m-30) REVERT: L 132 LYS cc_start: 0.7680 (mmmm) cc_final: 0.7416 (mmmm) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.5408 time to fit residues: 39.7896 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099902 restraints weight = 5585.661| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.23 r_work: 0.3199 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4127 Z= 0.152 Angle : 0.593 5.523 5620 Z= 0.308 Chirality : 0.045 0.193 634 Planarity : 0.004 0.040 706 Dihedral : 5.494 50.978 665 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.60 % Allowed : 19.91 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.37 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.81 (0.35), residues: 214 loop : -0.17 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.012 0.001 TYR A 28 PHE 0.021 0.002 PHE H 70 TRP 0.014 0.002 TRP L 60 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4117) covalent geometry : angle 0.57278 ( 5594) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.64342 ( 8) hydrogen bonds : bond 0.03472 ( 153) hydrogen bonds : angle 5.67350 ( 399) link_BETA1-4 : bond 0.00279 ( 1) link_BETA1-4 : angle 1.23690 ( 3) link_NAG-ASN : bond 0.00204 ( 5) link_NAG-ASN : angle 2.76507 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.207 Fit side-chains REVERT: A 14 GLN cc_start: 0.7763 (mt0) cc_final: 0.7323 (mt0) REVERT: A 15 CYS cc_start: 0.8228 (m) cc_final: 0.7985 (m) REVERT: A 80 ASP cc_start: 0.6787 (t0) cc_final: 0.6333 (t0) REVERT: A 131 CYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7789 (m) REVERT: A 137 ASN cc_start: 0.8507 (m110) cc_final: 0.8101 (t0) REVERT: A 169 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 177 MET cc_start: 0.8017 (pmt) cc_final: 0.7647 (pmt) REVERT: A 211 ASN cc_start: 0.8897 (p0) cc_final: 0.8669 (p0) REVERT: H 58 GLN cc_start: 0.7208 (tt0) cc_final: 0.6960 (tt0) REVERT: H 65 GLU cc_start: 0.7428 (pt0) cc_final: 0.7000 (pt0) REVERT: H 100 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7086 (ttp) REVERT: H 135 ASP cc_start: 0.8290 (m-30) cc_final: 0.7983 (m-30) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.5564 time to fit residues: 40.2657 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099042 restraints weight = 5622.712| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.26 r_work: 0.3187 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4127 Z= 0.168 Angle : 0.612 6.157 5620 Z= 0.318 Chirality : 0.045 0.197 634 Planarity : 0.004 0.039 706 Dihedral : 5.595 50.909 665 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.06 % Allowed : 19.45 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.32 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.79 (0.35), residues: 214 loop : -0.22 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 190 TYR 0.012 0.001 TYR A 28 PHE 0.021 0.002 PHE H 70 TRP 0.015 0.002 TRP L 60 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4117) covalent geometry : angle 0.59196 ( 5594) SS BOND : bond 0.00342 ( 4) SS BOND : angle 1.65893 ( 8) hydrogen bonds : bond 0.03562 ( 153) hydrogen bonds : angle 5.72286 ( 399) link_BETA1-4 : bond 0.00250 ( 1) link_BETA1-4 : angle 1.20809 ( 3) link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 2.83465 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.38 seconds wall clock time: 40 minutes 48.99 seconds (2448.99 seconds total)