Starting phenix.real_space_refine on Wed Jul 23 19:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_27526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_27526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_27526.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_27526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2025/8dm4_27526.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.12, per 1000 atoms: 1.03 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: 0.99 Conformation dependent library (CDL) restraints added in 515.4 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: 0.50 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: 1.20 Time building geometry restraints manager: 1.19 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.680 Find NCS groups from input model: 0.040 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:15.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.003 PHE A 175 TYR 0.032 0.003 TYR A 145 ARG 0.016 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 5) link_NAG-ASN : angle 3.54620 ( 15) link_BETA1-4 : bond 0.01012 ( 1) link_BETA1-4 : angle 2.50579 ( 3) hydrogen bonds : bond 0.07968 ( 153) hydrogen bonds : angle 6.59570 ( 399) SS BOND : bond 0.00341 ( 4) SS BOND : angle 2.19227 ( 8) covalent geometry : bond 0.00609 ( 4117) covalent geometry : angle 0.90354 ( 5594) *********************** 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 : 0.452 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: 1.3280 time to fit residues: 138.0137 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 : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.144334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100357 restraints weight = 5622.689| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.23 r_work: 0.3209 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4127 Z= 0.160 Angle : 0.620 8.442 5620 Z= 0.316 Chirality : 0.045 0.214 634 Planarity : 0.004 0.055 706 Dihedral : 7.413 57.756 665 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 10.76 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.76 (0.35), residues: 215 loop : -0.25 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 175 TYR 0.014 0.002 TYR A 28 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 2.96225 ( 15) link_BETA1-4 : bond 0.00115 ( 1) link_BETA1-4 : angle 1.47537 ( 3) hydrogen bonds : bond 0.03781 ( 153) hydrogen bonds : angle 6.02533 ( 399) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.54217 ( 8) covalent geometry : bond 0.00363 ( 4117) covalent geometry : angle 0.59849 ( 5594) *********************** 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 : 0.425 Fit side-chains REVERT: A 80 ASP cc_start: 0.6620 (t0) cc_final: 0.6164 (t0) REVERT: A 115 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8206 (mm110) REVERT: A 169 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 173 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: H 65 GLU cc_start: 0.7384 (pt0) cc_final: 0.6722 (pm20) REVERT: H 100 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6671 (ttp) REVERT: H 109 ASP cc_start: 0.7164 (t0) cc_final: 0.6914 (t0) REVERT: H 131 TYR cc_start: 0.8153 (t80) cc_final: 0.7896 (t80) REVERT: H 134 MET cc_start: 0.8768 (mtm) cc_final: 0.8457 (mpp) REVERT: L 132 LYS cc_start: 0.7608 (mmmm) cc_final: 0.7387 (mmmm) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 1.3662 time to fit residues: 100.0073 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 : 0.431 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.144856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101594 restraints weight = 5495.705| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.16 r_work: 0.3225 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4127 Z= 0.119 Angle : 0.562 5.492 5620 Z= 0.291 Chirality : 0.044 0.193 634 Planarity : 0.004 0.045 706 Dihedral : 6.667 56.355 665 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 12.81 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.85 (0.35), residues: 213 loop : -0.08 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.013 0.001 PHE A 175 TYR 0.012 0.001 TYR A 28 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 5) link_NAG-ASN : angle 2.69435 ( 15) link_BETA1-4 : bond 0.00229 ( 1) link_BETA1-4 : angle 1.07985 ( 3) hydrogen bonds : bond 0.03443 ( 153) hydrogen bonds : angle 5.74036 ( 399) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.35592 ( 8) covalent geometry : bond 0.00269 ( 4117) covalent geometry : angle 0.54278 ( 5594) *********************** 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: 11 poor density : 71 time to evaluate : 0.435 Fit side-chains REVERT: A 14 GLN cc_start: 0.7720 (mt0) cc_final: 0.7496 (mt0) REVERT: A 80 ASP cc_start: 0.6634 (t0) cc_final: 0.6175 (t0) REVERT: A 137 ASN cc_start: 0.8437 (m110) cc_final: 0.7949 (t0) REVERT: A 169 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: A 173 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: A 177 MET cc_start: 0.7964 (pmt) cc_final: 0.7619 (pmt) REVERT: H 65 GLU cc_start: 0.7447 (pt0) cc_final: 0.7152 (pt0) REVERT: H 78 MET cc_start: 0.7040 (tpp) cc_final: 0.6123 (tpt) REVERT: H 100 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6608 (ttp) REVERT: H 109 ASP cc_start: 0.7192 (t0) cc_final: 0.6938 (t0) REVERT: H 131 TYR cc_start: 0.8221 (t80) cc_final: 0.7969 (t80) REVERT: H 134 MET cc_start: 0.8746 (mtm) cc_final: 0.8500 (mpp) REVERT: L 117 THR cc_start: 0.8324 (p) cc_final: 0.8069 (p) REVERT: L 132 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7290 (mmmm) outliers start: 11 outliers final: 4 residues processed: 74 average time/residue: 1.4461 time to fit residues: 110.4126 Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 30 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 45 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.143851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100614 restraints weight = 5553.749| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.16 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4127 Z= 0.144 Angle : 0.568 5.423 5620 Z= 0.293 Chirality : 0.044 0.193 634 Planarity : 0.004 0.042 706 Dihedral : 6.289 52.414 665 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.75 % Allowed : 14.19 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.87 (0.35), residues: 213 loop : -0.03 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.017 0.001 PHE A 175 TYR 0.012 0.001 TYR A 28 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 5) link_NAG-ASN : angle 2.73444 ( 15) link_BETA1-4 : bond 0.00145 ( 1) link_BETA1-4 : angle 0.99998 ( 3) hydrogen bonds : bond 0.03457 ( 153) hydrogen bonds : angle 5.70843 ( 399) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.73448 ( 8) covalent geometry : bond 0.00329 ( 4117) covalent geometry : angle 0.54739 ( 5594) *********************** 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 : 0.435 Fit side-chains REVERT: A 14 GLN cc_start: 0.7702 (mt0) cc_final: 0.7473 (mt0) REVERT: A 80 ASP cc_start: 0.6659 (t0) cc_final: 0.6236 (t0) REVERT: A 115 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8175 (mm110) REVERT: A 137 ASN cc_start: 0.8446 (m110) cc_final: 0.7975 (t0) REVERT: A 169 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 173 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: A 177 MET cc_start: 0.7988 (pmt) cc_final: 0.7611 (pmt) REVERT: H 65 GLU cc_start: 0.7454 (pt0) cc_final: 0.7110 (pt0) REVERT: H 78 MET cc_start: 0.7041 (tpp) cc_final: 0.6141 (tpt) REVERT: H 100 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6869 (ttp) REVERT: H 109 ASP cc_start: 0.7205 (t0) cc_final: 0.7000 (t0) REVERT: H 134 MET cc_start: 0.8738 (mtm) cc_final: 0.8469 (mpp) REVERT: H 135 ASP cc_start: 0.8312 (m-30) cc_final: 0.8095 (m-30) outliers start: 12 outliers final: 3 residues processed: 73 average time/residue: 1.1873 time to fit residues: 89.7037 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 : 0.418 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097401 restraints weight = 5662.474| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.19 r_work: 0.3166 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4127 Z= 0.240 Angle : 0.642 7.079 5620 Z= 0.329 Chirality : 0.047 0.206 634 Planarity : 0.004 0.041 706 Dihedral : 6.342 50.179 665 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 15.56 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.87 (0.35), residues: 212 loop : -0.16 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.027 0.002 PHE A 175 TYR 0.015 0.002 TYR A 28 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 3.11199 ( 15) link_BETA1-4 : bond 0.00102 ( 1) link_BETA1-4 : angle 1.20060 ( 3) hydrogen bonds : bond 0.03936 ( 153) hydrogen bonds : angle 5.92509 ( 399) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.84645 ( 8) covalent geometry : bond 0.00560 ( 4117) covalent geometry : angle 0.61812 ( 5594) *********************** 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 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.904 Fit side-chains REVERT: A 15 CYS cc_start: 0.8267 (m) cc_final: 0.8043 (m) REVERT: A 80 ASP cc_start: 0.6733 (t0) cc_final: 0.6309 (t0) REVERT: A 137 ASN cc_start: 0.8485 (m110) cc_final: 0.8079 (t0) REVERT: A 169 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: A 173 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: H 65 GLU cc_start: 0.7577 (pt0) cc_final: 0.7231 (pt0) REVERT: H 78 MET cc_start: 0.7087 (tpp) cc_final: 0.6186 (tpt) REVERT: H 100 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7330 (ttp) REVERT: H 134 MET cc_start: 0.8838 (mtm) cc_final: 0.8522 (mpp) REVERT: L 132 LYS cc_start: 0.7708 (mmmm) cc_final: 0.7348 (mmmm) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 1.7605 time to fit residues: 127.4881 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 : 0.457 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain L residue 117 THR 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 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.142629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099269 restraints weight = 5571.791| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.17 r_work: 0.3200 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2373 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= 0.163 Angle : 0.594 5.962 5620 Z= 0.308 Chirality : 0.045 0.194 634 Planarity : 0.004 0.039 706 Dihedral : 5.950 51.387 665 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 15.79 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.92 (0.35), residues: 212 loop : -0.14 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.019 0.002 PHE A 175 TYR 0.013 0.001 TYR A 28 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 5) link_NAG-ASN : angle 2.91899 ( 15) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.10237 ( 3) hydrogen bonds : bond 0.03632 ( 153) hydrogen bonds : angle 5.76367 ( 399) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.66853 ( 8) covalent geometry : bond 0.00372 ( 4117) covalent geometry : angle 0.57166 ( 5594) *********************** 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 79 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.500 Fit side-chains REVERT: A 14 GLN cc_start: 0.7858 (mt0) cc_final: 0.7408 (mt0) REVERT: A 15 CYS cc_start: 0.8211 (m) cc_final: 0.7960 (m) REVERT: A 80 ASP cc_start: 0.6702 (t0) cc_final: 0.6265 (t0) REVERT: A 137 ASN cc_start: 0.8483 (m110) cc_final: 0.8066 (t0) REVERT: A 169 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 173 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: H 48 LEU cc_start: 0.8027 (tp) cc_final: 0.7810 (mt) REVERT: H 65 GLU cc_start: 0.7478 (pt0) cc_final: 0.7092 (pt0) REVERT: H 78 MET cc_start: 0.6995 (tpp) cc_final: 0.6098 (tpt) REVERT: H 100 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7154 (ttp) REVERT: L 132 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7397 (mmmm) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 1.7207 time to fit residues: 130.2264 Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.142520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099387 restraints weight = 5572.539| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.17 r_work: 0.3194 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2506 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= 0.155 Angle : 0.586 5.759 5620 Z= 0.304 Chirality : 0.045 0.192 634 Planarity : 0.004 0.039 706 Dihedral : 5.732 51.164 665 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 220 loop : -0.10 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.018 0.002 PHE A 175 TYR 0.012 0.001 TYR A 28 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 5) link_NAG-ASN : angle 2.86620 ( 15) link_BETA1-4 : bond 0.00290 ( 1) link_BETA1-4 : angle 1.16999 ( 3) hydrogen bonds : bond 0.03564 ( 153) hydrogen bonds : angle 5.70401 ( 399) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.68007 ( 8) covalent geometry : bond 0.00354 ( 4117) covalent geometry : angle 0.56387 ( 5594) *********************** 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 79 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.483 Fit side-chains REVERT: A 14 GLN cc_start: 0.7834 (mt0) cc_final: 0.7402 (mt0) REVERT: A 15 CYS cc_start: 0.8253 (m) cc_final: 0.8009 (m) REVERT: A 80 ASP cc_start: 0.6719 (t0) cc_final: 0.6296 (t0) REVERT: A 131 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7772 (m) REVERT: A 137 ASN cc_start: 0.8480 (m110) cc_final: 0.8108 (t0) REVERT: A 169 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 173 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: A 177 MET cc_start: 0.8044 (pmt) cc_final: 0.7739 (pmt) REVERT: H 48 LEU cc_start: 0.8072 (tp) cc_final: 0.7853 (mt) REVERT: H 58 GLN cc_start: 0.7417 (tt0) cc_final: 0.7198 (tt0) REVERT: H 65 GLU cc_start: 0.7548 (pt0) cc_final: 0.7157 (pt0) REVERT: H 78 MET cc_start: 0.7160 (tpp) cc_final: 0.6125 (tpt) REVERT: H 100 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7164 (ttp) REVERT: L 132 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7381 (mmmm) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 1.1900 time to fit residues: 88.8548 Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.143530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100521 restraints weight = 5539.357| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.16 r_work: 0.3217 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2565 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= 0.136 Angle : 0.581 5.931 5620 Z= 0.302 Chirality : 0.044 0.190 634 Planarity : 0.004 0.038 706 Dihedral : 5.533 51.340 665 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.29 % Allowed : 18.31 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.91 (0.35), residues: 214 loop : -0.13 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.007 0.001 HIS A 245 PHE 0.018 0.001 PHE H 70 TYR 0.011 0.001 TYR A 28 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 2.75321 ( 15) link_BETA1-4 : bond 0.00288 ( 1) link_BETA1-4 : angle 1.18392 ( 3) hydrogen bonds : bond 0.03441 ( 153) hydrogen bonds : angle 5.59179 ( 399) SS BOND : bond 0.00329 ( 4) SS BOND : angle 1.60776 ( 8) covalent geometry : bond 0.00308 ( 4117) covalent geometry : angle 0.56045 ( 5594) *********************** 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: 10 poor density : 67 time to evaluate : 0.443 Fit side-chains REVERT: A 14 GLN cc_start: 0.7801 (mt0) cc_final: 0.7392 (mt0) REVERT: A 15 CYS cc_start: 0.8198 (m) cc_final: 0.7959 (m) REVERT: A 80 ASP cc_start: 0.6710 (t0) cc_final: 0.6269 (t0) REVERT: A 131 CYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 137 ASN cc_start: 0.8498 (m110) cc_final: 0.8108 (t0) REVERT: A 169 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: A 173 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: A 177 MET cc_start: 0.8036 (pmt) cc_final: 0.7754 (pmt) REVERT: H 48 LEU cc_start: 0.7915 (tp) cc_final: 0.7655 (mt) REVERT: H 53 MET cc_start: 0.7914 (tpp) cc_final: 0.7565 (tpt) REVERT: H 58 GLN cc_start: 0.7246 (tt0) cc_final: 0.7041 (tt0) REVERT: H 65 GLU cc_start: 0.7486 (pt0) cc_final: 0.7096 (pt0) REVERT: H 78 MET cc_start: 0.7128 (tpp) cc_final: 0.6083 (tpt) REVERT: H 100 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7037 (ttp) REVERT: L 24 MET cc_start: 0.7014 (mmt) cc_final: 0.6336 (mmt) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 1.0729 time to fit residues: 79.1600 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.142588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099216 restraints weight = 5597.006| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.25 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4127 Z= 0.163 Angle : 0.594 5.684 5620 Z= 0.308 Chirality : 0.045 0.194 634 Planarity : 0.004 0.038 706 Dihedral : 5.573 51.002 665 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.52 % Allowed : 18.76 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.90 (0.35), residues: 212 loop : -0.21 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.001 0.000 HIS A 49 PHE 0.020 0.002 PHE H 70 TYR 0.012 0.001 TYR A 28 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 5) link_NAG-ASN : angle 2.82623 ( 15) link_BETA1-4 : bond 0.00269 ( 1) link_BETA1-4 : angle 1.21020 ( 3) hydrogen bonds : bond 0.03533 ( 153) hydrogen bonds : angle 5.64852 ( 399) SS BOND : bond 0.00347 ( 4) SS BOND : angle 1.64805 ( 8) covalent geometry : bond 0.00377 ( 4117) covalent geometry : angle 0.57314 ( 5594) *********************** 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: 11 poor density : 64 time to evaluate : 0.478 Fit side-chains REVERT: A 14 GLN cc_start: 0.7766 (mt0) cc_final: 0.7332 (mt0) REVERT: A 15 CYS cc_start: 0.8210 (m) cc_final: 0.7955 (m) REVERT: A 80 ASP cc_start: 0.6697 (t0) cc_final: 0.6219 (t0) REVERT: A 131 CYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 137 ASN cc_start: 0.8515 (m110) cc_final: 0.8083 (t0) REVERT: A 169 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: A 173 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: A 177 MET cc_start: 0.8008 (pmt) cc_final: 0.7693 (pmt) REVERT: H 48 LEU cc_start: 0.7779 (tp) cc_final: 0.7574 (mt) REVERT: H 58 GLN cc_start: 0.7195 (tt0) cc_final: 0.6983 (tt0) REVERT: H 65 GLU cc_start: 0.7399 (pt0) cc_final: 0.6988 (pt0) REVERT: H 78 MET cc_start: 0.7049 (tpp) cc_final: 0.6006 (tpt) REVERT: H 100 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6998 (ttp) REVERT: L 24 MET cc_start: 0.7106 (mmt) cc_final: 0.6482 (mmt) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 1.3010 time to fit residues: 94.9845 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.143163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100236 restraints weight = 5587.221| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.24 r_work: 0.3206 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2640 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= 0.137 Angle : 0.581 5.436 5620 Z= 0.302 Chirality : 0.044 0.191 634 Planarity : 0.003 0.038 706 Dihedral : 5.480 51.348 665 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.06 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 212 loop : -0.19 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.002 0.000 HIS A 245 PHE 0.020 0.001 PHE H 70 TYR 0.011 0.001 TYR H 132 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 5) link_NAG-ASN : angle 2.73880 ( 15) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 1.21450 ( 3) hydrogen bonds : bond 0.03386 ( 153) hydrogen bonds : angle 5.58964 ( 399) SS BOND : bond 0.00326 ( 4) SS BOND : angle 1.60584 ( 8) covalent geometry : bond 0.00312 ( 4117) covalent geometry : angle 0.56129 ( 5594) ********************** 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 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.438 Fit side-chains REVERT: A 14 GLN cc_start: 0.7759 (mt0) cc_final: 0.7347 (mt0) REVERT: A 15 CYS cc_start: 0.8217 (m) cc_final: 0.7962 (m) REVERT: A 80 ASP cc_start: 0.6701 (t0) cc_final: 0.6229 (t0) REVERT: A 131 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 137 ASN cc_start: 0.8508 (m110) cc_final: 0.8087 (t0) REVERT: A 169 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: A 173 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: A 177 MET cc_start: 0.8008 (pmt) cc_final: 0.7700 (pmt) REVERT: H 48 LEU cc_start: 0.7735 (tp) cc_final: 0.7481 (mt) REVERT: H 53 MET cc_start: 0.7841 (tpp) cc_final: 0.7497 (tpt) REVERT: H 58 GLN cc_start: 0.7212 (tt0) cc_final: 0.6986 (tt0) REVERT: H 65 GLU cc_start: 0.7389 (pt0) cc_final: 0.6982 (pt0) REVERT: H 78 MET cc_start: 0.7085 (tpp) cc_final: 0.6045 (tpt) REVERT: H 100 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6934 (ttp) REVERT: L 24 MET cc_start: 0.6986 (mmt) cc_final: 0.6393 (mmt) REVERT: L 132 LYS cc_start: 0.7651 (mmmm) cc_final: 0.7318 (mmmm) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 1.1357 time to fit residues: 82.4514 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.143018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100127 restraints weight = 5549.085| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.23 r_work: 0.3203 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2691 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= 0.145 Angle : 0.585 5.459 5620 Z= 0.304 Chirality : 0.045 0.192 634 Planarity : 0.003 0.038 706 Dihedral : 5.464 51.053 665 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.29 % Allowed : 18.99 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.85 (0.35), residues: 212 loop : -0.19 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.021 0.002 PHE H 70 TYR 0.011 0.001 TYR H 132 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 5) link_NAG-ASN : angle 2.73877 ( 15) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 1.23577 ( 3) hydrogen bonds : bond 0.03420 ( 153) hydrogen bonds : angle 5.60150 ( 399) SS BOND : bond 0.00327 ( 4) SS BOND : angle 1.63655 ( 8) covalent geometry : bond 0.00333 ( 4117) covalent geometry : angle 0.56456 ( 5594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5131.69 seconds wall clock time: 92 minutes 56.46 seconds (5576.46 seconds total)