Starting phenix.real_space_refine on Wed Jul 23 19:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.map" model { file = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2025/8dls_27514.cif" } resolution = 2.66 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= -0.000 sd= 0.016 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 2566 2.51 5 N 648 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2081 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.12, per 1000 atoms: 1.03 Number of scatterers: 4017 At special positions: 0 Unit cell: (95, 61, 101, 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 785 8.00 N 648 7.00 C 2566 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=2.03 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 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 484.3 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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: 3.910A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.963A pdb=" N VAL L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.924A 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: 3.764A 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 removed outlier: 3.606A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.738A 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 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (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: 3.758A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 357 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: 1.11 Time building geometry restraints manager: 1.24 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: 1235 1.34 - 1.46: 1022 1.46 - 1.58: 1834 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 4118 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C ARG A 102 " pdb=" N GLY A 103 " ideal model delta sigma weight residual 1.327 1.307 0.020 1.11e-02 8.12e+03 3.25e+00 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 5450 2.47 - 4.95: 130 4.95 - 7.42: 14 7.42 - 9.90: 1 9.90 - 12.37: 2 Bond angle restraints: 5597 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 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA LEU H 127 " pdb=" CB LEU H 127 " pdb=" CG LEU H 127 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C GLN H 139 " pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 122.73 119.73 3.00 9.30e-01 1.16e+00 1.04e+01 angle pdb=" CA THR L 56 " pdb=" CB THR L 56 " pdb=" CG2 THR L 56 " ideal model delta sigma weight residual 110.50 115.81 -5.31 1.70e+00 3.46e-01 9.77e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.64e+00 ... (remaining 5592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2319 17.40 - 34.79: 149 34.79 - 52.18: 26 52.18 - 69.57: 5 69.57 - 86.97: 5 Dihedral angle restraints: 2504 sinusoidal: 1066 harmonic: 1438 Sorted by residual: dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 572 0.097 - 0.193: 57 0.193 - 0.290: 3 0.290 - 0.386: 0 0.386 - 0.483: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+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 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 632 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.005 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 198 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" CG ASP A 198 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 198 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO L 84 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.035 5.00e-02 4.00e+02 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1088 2.81 - 3.33: 3098 3.33 - 3.86: 6567 3.86 - 4.38: 7546 4.38 - 4.90: 13461 Nonbonded interactions: 31760 Sorted by model distance: nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR H 124 " pdb=" O ASP H 126 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.362 3.040 nonbonded pdb=" O SER H 147 " pdb=" OG SER H 147 " model vdw 2.374 3.040 ... (remaining 31755 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: 86.520 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.720 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 0.057 4129 Z= 0.279 Angle : 0.982 14.060 5626 Z= 0.500 Chirality : 0.063 0.483 635 Planarity : 0.007 0.069 705 Dihedral : 12.285 86.966 1572 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.59 (0.37), residues: 483 helix: None (None), residues: 0 sheet: 0.15 (0.36), residues: 218 loop : -0.84 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.005 0.002 HIS L 51 PHE 0.028 0.003 PHE A 238 TYR 0.020 0.002 TYR A 160 ARG 0.014 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.01313 ( 6) link_NAG-ASN : angle 6.06365 ( 18) link_BETA1-4 : bond 0.01131 ( 1) link_BETA1-4 : angle 2.94365 ( 3) hydrogen bonds : bond 0.09359 ( 139) hydrogen bonds : angle 6.77791 ( 357) SS BOND : bond 0.00134 ( 4) SS BOND : angle 2.20868 ( 8) covalent geometry : bond 0.00614 ( 4118) covalent geometry : angle 0.91645 ( 5597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.476 Fit side-chains REVERT: A 15 CYS cc_start: 0.7351 (m) cc_final: 0.7117 (m) REVERT: A 153 MET cc_start: 0.8371 (mmt) cc_final: 0.8037 (mmm) REVERT: H 99 TYR cc_start: 0.7958 (m-80) cc_final: 0.7599 (m-80) REVERT: L 63 GLN cc_start: 0.8931 (tt0) cc_final: 0.8728 (tt0) REVERT: L 75 LYS cc_start: 0.8501 (mttt) cc_final: 0.8168 (mtpt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.0395 time to fit residues: 105.6876 Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN L 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080365 restraints weight = 6280.953| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.81 r_work: 0.2965 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4129 Z= 0.129 Angle : 0.641 10.449 5626 Z= 0.315 Chirality : 0.049 0.383 635 Planarity : 0.004 0.048 705 Dihedral : 6.150 50.541 684 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.84 % Allowed : 9.66 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.10 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.39 (0.36), residues: 213 loop : -0.38 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 175 TYR 0.009 0.001 TYR A 269 ARG 0.004 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 6) link_NAG-ASN : angle 4.03828 ( 18) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 1.48585 ( 3) hydrogen bonds : bond 0.03402 ( 139) hydrogen bonds : angle 6.00777 ( 357) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.34601 ( 8) covalent geometry : bond 0.00295 ( 4118) covalent geometry : angle 0.59773 ( 5597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.435 Fit side-chains REVERT: A 129 LYS cc_start: 0.8269 (ttmm) cc_final: 0.8019 (ttmm) REVERT: H 42 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8720 (tttp) REVERT: H 48 LEU cc_start: 0.8547 (tp) cc_final: 0.8192 (tt) REVERT: H 99 TYR cc_start: 0.8120 (m-80) cc_final: 0.7826 (m-80) REVERT: H 130 TYR cc_start: 0.8446 (m-80) cc_final: 0.8113 (m-80) REVERT: L 63 GLN cc_start: 0.8923 (tt0) cc_final: 0.8662 (tt0) REVERT: L 70 ARG cc_start: 0.8643 (ptt180) cc_final: 0.8421 (ppt170) REVERT: L 75 LYS cc_start: 0.8368 (mttt) cc_final: 0.8078 (mmmt) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 1.0121 time to fit residues: 91.5741 Evaluate side-chains 86 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 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 39 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.0050 chunk 35 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080439 restraints weight = 6350.620| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.85 r_work: 0.2967 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4129 Z= 0.121 Angle : 0.609 10.005 5626 Z= 0.299 Chirality : 0.047 0.341 635 Planarity : 0.004 0.042 705 Dihedral : 5.793 50.389 684 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.84 % Allowed : 12.18 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.17 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.48 (0.36), residues: 215 loop : -0.12 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 PHE 0.016 0.001 PHE L 96 TYR 0.012 0.001 TYR H 132 ARG 0.004 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00860 ( 6) link_NAG-ASN : angle 3.50720 ( 18) link_BETA1-4 : bond 0.00402 ( 1) link_BETA1-4 : angle 1.48840 ( 3) hydrogen bonds : bond 0.03103 ( 139) hydrogen bonds : angle 5.78945 ( 357) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.17281 ( 8) covalent geometry : bond 0.00280 ( 4118) covalent geometry : angle 0.57413 ( 5597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.449 Fit side-chains REVERT: A 214 ARG cc_start: 0.7819 (tpp-160) cc_final: 0.7502 (tpp-160) REVERT: H 48 LEU cc_start: 0.8561 (tp) cc_final: 0.8170 (tt) REVERT: H 50 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8009 (mp0) REVERT: H 65 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: H 83 PHE cc_start: 0.8424 (m-10) cc_final: 0.8065 (m-10) REVERT: H 130 TYR cc_start: 0.8437 (m-80) cc_final: 0.7928 (m-80) REVERT: L 63 GLN cc_start: 0.8895 (tt0) cc_final: 0.8606 (tt0) outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 1.1746 time to fit residues: 104.9455 Evaluate side-chains 86 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN 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 19 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079225 restraints weight = 6401.525| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.83 r_work: 0.2951 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4129 Z= 0.146 Angle : 0.616 10.864 5626 Z= 0.301 Chirality : 0.047 0.333 635 Planarity : 0.004 0.041 705 Dihedral : 5.672 49.528 684 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.45 % Allowed : 13.33 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.32 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.49 (0.36), residues: 215 loop : 0.09 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 PHE 0.016 0.001 PHE L 96 TYR 0.009 0.001 TYR A 269 ARG 0.004 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 6) link_NAG-ASN : angle 3.37280 ( 18) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 1.35734 ( 3) hydrogen bonds : bond 0.03081 ( 139) hydrogen bonds : angle 5.66075 ( 357) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.15666 ( 8) covalent geometry : bond 0.00342 ( 4118) covalent geometry : angle 0.58475 ( 5597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7540 (tpp-160) REVERT: A 215 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: H 48 LEU cc_start: 0.8624 (tp) cc_final: 0.8225 (tt) REVERT: H 50 GLU cc_start: 0.8731 (mt-10) cc_final: 0.7896 (mp0) REVERT: H 65 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: H 130 TYR cc_start: 0.8503 (m-80) cc_final: 0.8003 (m-80) REVERT: L 63 GLN cc_start: 0.8988 (tt0) cc_final: 0.8719 (tt0) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 1.4001 time to fit residues: 127.0851 Evaluate side-chains 89 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 103 VAL 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 35 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.122117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079857 restraints weight = 6565.500| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.85 r_work: 0.2957 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4129 Z= 0.128 Angle : 0.616 11.404 5626 Z= 0.300 Chirality : 0.047 0.325 635 Planarity : 0.004 0.041 705 Dihedral : 5.575 49.707 684 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.22 % Allowed : 14.25 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.42 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.62 (0.37), residues: 204 loop : 0.11 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.013 0.001 PHE L 96 TYR 0.012 0.001 TYR H 79 ARG 0.005 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00804 ( 6) link_NAG-ASN : angle 3.20304 ( 18) link_BETA1-4 : bond 0.00429 ( 1) link_BETA1-4 : angle 1.34590 ( 3) hydrogen bonds : bond 0.02982 ( 139) hydrogen bonds : angle 5.62365 ( 357) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.33560 ( 8) covalent geometry : bond 0.00301 ( 4118) covalent geometry : angle 0.58776 ( 5597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.649 Fit side-chains REVERT: A 214 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7533 (tpp-160) REVERT: A 215 ASP cc_start: 0.7868 (m-30) cc_final: 0.7219 (m-30) REVERT: H 48 LEU cc_start: 0.8569 (tp) cc_final: 0.8189 (tt) REVERT: H 65 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: H 130 TYR cc_start: 0.8526 (m-80) cc_final: 0.8056 (m-80) REVERT: L 63 GLN cc_start: 0.8959 (tt0) cc_final: 0.8657 (tt0) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 2.0931 time to fit residues: 178.6856 Evaluate side-chains 82 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL 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 32 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078482 restraints weight = 6437.269| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.81 r_work: 0.2940 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4129 Z= 0.167 Angle : 0.632 11.841 5626 Z= 0.309 Chirality : 0.047 0.327 635 Planarity : 0.004 0.040 705 Dihedral : 5.575 48.097 684 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.91 % Allowed : 14.25 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.65 (0.38), residues: 198 loop : 0.16 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.016 0.001 PHE A 175 TYR 0.009 0.001 TYR A 269 ARG 0.006 0.001 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 6) link_NAG-ASN : angle 3.21586 ( 18) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 1.22698 ( 3) hydrogen bonds : bond 0.03108 ( 139) hydrogen bonds : angle 5.60308 ( 357) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.26900 ( 8) covalent geometry : bond 0.00397 ( 4118) covalent geometry : angle 0.60378 ( 5597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8636 (t0) cc_final: 0.8432 (t0) REVERT: A 215 ASP cc_start: 0.7868 (m-30) cc_final: 0.7491 (m-30) REVERT: H 48 LEU cc_start: 0.8629 (tp) cc_final: 0.8269 (tt) REVERT: H 65 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: H 100 MET cc_start: 0.8081 (ttp) cc_final: 0.7807 (ttt) REVERT: H 130 TYR cc_start: 0.8622 (m-80) cc_final: 0.8163 (m-80) REVERT: L 55 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7266 (p0) REVERT: L 63 GLN cc_start: 0.8997 (tt0) cc_final: 0.8680 (tt0) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.9763 time to fit residues: 81.3055 Evaluate side-chains 89 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078900 restraints weight = 6446.172| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.80 r_work: 0.2941 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4129 Z= 0.143 Angle : 0.618 12.714 5626 Z= 0.301 Chirality : 0.047 0.324 635 Planarity : 0.004 0.041 705 Dihedral : 5.516 48.494 684 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.60 % Allowed : 14.94 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.53 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.69 (0.38), residues: 203 loop : 0.19 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 PHE 0.017 0.001 PHE H 83 TYR 0.016 0.001 TYR H 99 ARG 0.006 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 6) link_NAG-ASN : angle 3.12679 ( 18) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 1.23757 ( 3) hydrogen bonds : bond 0.02994 ( 139) hydrogen bonds : angle 5.56580 ( 357) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.28800 ( 8) covalent geometry : bond 0.00339 ( 4118) covalent geometry : angle 0.59062 ( 5597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: H 31 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7042 (ptpp) REVERT: H 48 LEU cc_start: 0.8537 (tp) cc_final: 0.8202 (tt) REVERT: H 65 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: H 100 MET cc_start: 0.8139 (ttp) cc_final: 0.7742 (tmt) REVERT: H 130 TYR cc_start: 0.8630 (m-80) cc_final: 0.8215 (m-80) REVERT: L 55 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7200 (p0) REVERT: L 63 GLN cc_start: 0.8965 (tt0) cc_final: 0.8679 (tt0) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 1.0166 time to fit residues: 88.9310 Evaluate side-chains 92 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078498 restraints weight = 6390.748| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.77 r_work: 0.2935 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4129 Z= 0.161 Angle : 0.641 13.439 5626 Z= 0.316 Chirality : 0.047 0.323 635 Planarity : 0.004 0.041 705 Dihedral : 5.587 47.799 684 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.91 % Allowed : 16.55 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.58 (0.39), residues: 192 loop : 0.14 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 PHE 0.015 0.001 PHE A 175 TYR 0.009 0.001 TYR A 269 ARG 0.006 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 6) link_NAG-ASN : angle 3.10935 ( 18) link_BETA1-4 : bond 0.00445 ( 1) link_BETA1-4 : angle 1.19614 ( 3) hydrogen bonds : bond 0.02987 ( 139) hydrogen bonds : angle 5.55415 ( 357) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.81598 ( 8) covalent geometry : bond 0.00384 ( 4118) covalent geometry : angle 0.61313 ( 5597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: H 48 LEU cc_start: 0.8573 (tp) cc_final: 0.8237 (tt) REVERT: H 65 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: L 55 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7286 (p0) REVERT: L 63 GLN cc_start: 0.8999 (tt0) cc_final: 0.8690 (tt0) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 1.2665 time to fit residues: 110.1330 Evaluate side-chains 93 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.120150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078011 restraints weight = 6519.469| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.78 r_work: 0.2928 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4129 Z= 0.180 Angle : 0.666 13.769 5626 Z= 0.329 Chirality : 0.048 0.316 635 Planarity : 0.004 0.042 705 Dihedral : 5.660 46.936 684 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.37 % Allowed : 16.55 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.57 (0.38), residues: 199 loop : 0.15 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.017 0.002 PHE A 175 TYR 0.015 0.001 TYR H 99 ARG 0.007 0.001 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 6) link_NAG-ASN : angle 3.09374 ( 18) link_BETA1-4 : bond 0.00473 ( 1) link_BETA1-4 : angle 1.16116 ( 3) hydrogen bonds : bond 0.03106 ( 139) hydrogen bonds : angle 5.60091 ( 357) SS BOND : bond 0.00109 ( 4) SS BOND : angle 1.54468 ( 8) covalent geometry : bond 0.00432 ( 4118) covalent geometry : angle 0.64141 ( 5597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.475 Fit side-chains REVERT: H 31 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7088 (ptpp) REVERT: H 48 LEU cc_start: 0.8568 (tp) cc_final: 0.8253 (tt) REVERT: H 65 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: H 130 TYR cc_start: 0.8679 (m-80) cc_final: 0.8259 (m-80) REVERT: L 55 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7304 (p0) REVERT: L 63 GLN cc_start: 0.9009 (tt0) cc_final: 0.8703 (tt0) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.9642 time to fit residues: 83.3915 Evaluate side-chains 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 4 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.079155 restraints weight = 6462.197| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.79 r_work: 0.2943 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4129 Z= 0.145 Angle : 0.662 13.980 5626 Z= 0.323 Chirality : 0.047 0.315 635 Planarity : 0.004 0.041 705 Dihedral : 5.588 47.970 684 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.99 % Allowed : 18.62 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.45 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.38), residues: 199 loop : 0.23 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 PHE 0.013 0.001 PHE A 175 TYR 0.015 0.001 TYR H 132 ARG 0.006 0.000 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 6) link_NAG-ASN : angle 3.02533 ( 18) link_BETA1-4 : bond 0.00487 ( 1) link_BETA1-4 : angle 1.21425 ( 3) hydrogen bonds : bond 0.02893 ( 139) hydrogen bonds : angle 5.61440 ( 357) SS BOND : bond 0.00123 ( 4) SS BOND : angle 1.32522 ( 8) covalent geometry : bond 0.00347 ( 4118) covalent geometry : angle 0.63895 ( 5597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: H 48 LEU cc_start: 0.8555 (tp) cc_final: 0.8181 (tt) REVERT: H 50 GLU cc_start: 0.8742 (mt-10) cc_final: 0.7948 (mp0) REVERT: H 65 GLU cc_start: 0.8467 (pt0) cc_final: 0.8110 (pt0) REVERT: H 130 TYR cc_start: 0.8632 (m-80) cc_final: 0.8217 (m-80) REVERT: L 55 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7168 (p0) REVERT: L 63 GLN cc_start: 0.8953 (tt0) cc_final: 0.8710 (tt0) REVERT: L 70 ARG cc_start: 0.8656 (ptt180) cc_final: 0.8149 (ppt-90) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.9820 time to fit residues: 84.9303 Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078634 restraints weight = 6405.578| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.79 r_work: 0.2941 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4129 Z= 0.149 Angle : 0.659 14.136 5626 Z= 0.321 Chirality : 0.047 0.315 635 Planarity : 0.004 0.041 705 Dihedral : 5.563 47.773 684 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.76 % Allowed : 18.85 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.56 (0.38), residues: 199 loop : 0.23 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.014 0.001 PHE A 175 TYR 0.017 0.001 TYR H 99 ARG 0.012 0.001 ARG L 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 6) link_NAG-ASN : angle 3.02300 ( 18) link_BETA1-4 : bond 0.00480 ( 1) link_BETA1-4 : angle 1.20374 ( 3) hydrogen bonds : bond 0.02920 ( 139) hydrogen bonds : angle 5.58878 ( 357) SS BOND : bond 0.00113 ( 4) SS BOND : angle 1.26139 ( 8) covalent geometry : bond 0.00357 ( 4118) covalent geometry : angle 0.63578 ( 5597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5017.94 seconds wall clock time: 91 minutes 7.72 seconds (5467.72 seconds total)