Starting phenix.real_space_refine on Sun Apr 27 09:38:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.map" model { file = "/net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eaj_47833/04_2025/9eaj_47833.cif" } resolution = 3.2 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= 0.009 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 24 5.16 5 C 3432 2.51 5 N 843 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2906 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain breaks: 3 Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 561 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 4 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 835 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.32, per 1000 atoms: 0.82 Number of scatterers: 5246 At special positions: 0 Unit cell: (64.74, 97.11, 138.61, 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 24 16.00 O 947 8.00 N 843 7.00 C 3432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " 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 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 667.4 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 50.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.714A pdb=" N SER A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 90 removed outlier: 3.744A pdb=" N THR A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.533A pdb=" N MET A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.539A pdb=" N CYS A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 244 Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.704A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.185A pdb=" N HIS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.008A pdb=" N ASN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 1236 removed outlier: 3.514A pdb=" N LYS A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A1235 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1268 removed outlier: 3.540A pdb=" N LYS A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) Proline residue: A1255 - end of helix Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1283 through 1292 removed outlier: 3.627A pdb=" N TYR A1292 " --> pdb=" O ILE A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1306 removed outlier: 3.786A pdb=" N LEU A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Proline residue: A1299 - end of helix removed outlier: 3.954A pdb=" N TYR A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.689A pdb=" N TRP C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.156A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 8.165A pdb=" N VAL B 109 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 182 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.545A pdb=" N TRP B 35 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET B 33 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.582A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.411A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 14 314 hydrogen bonds defined for protein. 891 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: 1.51 Time building geometry restraints manager: 1.46 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: 1574 1.34 - 1.45: 946 1.45 - 1.57: 2819 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5375 Sorted by residual: bond pdb=" CB TRP A 232 " pdb=" CG TRP A 232 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.62e-01 bond pdb=" CG LEU A 319 " pdb=" CD1 LEU A 319 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.36e-01 bond pdb=" CB MET A 258 " pdb=" CG MET A 258 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" CB TRP C 102 " pdb=" CG TRP C 102 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.41e-01 bond pdb=" CE2 PHE C 114 " pdb=" CZ PHE C 114 " ideal model delta sigma weight residual 1.382 1.358 0.024 3.00e-02 1.11e+03 6.25e-01 ... (remaining 5370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7204 1.63 - 3.26: 77 3.26 - 4.89: 13 4.89 - 6.52: 7 6.52 - 8.15: 1 Bond angle restraints: 7302 Sorted by residual: angle pdb=" CA TRP A 232 " pdb=" CB TRP A 232 " pdb=" CG TRP A 232 " ideal model delta sigma weight residual 113.60 108.51 5.09 1.90e+00 2.77e-01 7.18e+00 angle pdb=" CA LEU A 319 " pdb=" CB LEU A 319 " pdb=" CG LEU A 319 " ideal model delta sigma weight residual 116.30 124.45 -8.15 3.50e+00 8.16e-02 5.42e+00 angle pdb=" CA TYR D 50 " pdb=" CB TYR D 50 " pdb=" CG TYR D 50 " ideal model delta sigma weight residual 113.90 117.64 -3.74 1.80e+00 3.09e-01 4.32e+00 angle pdb=" N SER D 51 " pdb=" CA SER D 51 " pdb=" C SER D 51 " ideal model delta sigma weight residual 109.79 106.87 2.92 1.56e+00 4.11e-01 3.51e+00 angle pdb=" C ASN A 231 " pdb=" N TRP A 232 " pdb=" CA TRP A 232 " ideal model delta sigma weight residual 120.31 117.53 2.78 1.52e+00 4.33e-01 3.35e+00 ... (remaining 7297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2922 17.92 - 35.85: 164 35.85 - 53.77: 32 53.77 - 71.69: 9 71.69 - 89.62: 3 Dihedral angle restraints: 3130 sinusoidal: 1193 harmonic: 1937 Sorted by residual: dihedral pdb=" N ASN A 168 " pdb=" CA ASN A 168 " pdb=" CB ASN A 168 " pdb=" CG ASN A 168 " ideal model delta sinusoidal sigma weight residual -60.00 -119.35 59.35 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG D 25 " pdb=" CA ARG D 25 " pdb=" CB ARG D 25 " pdb=" CG ARG D 25 " ideal model delta sinusoidal sigma weight residual -180.00 -124.79 -55.21 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" CB GLU B 45 " pdb=" CG GLU B 45 " pdb=" CD GLU B 45 " pdb=" OE1 GLU B 45 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 479 0.029 - 0.057: 241 0.057 - 0.086: 73 0.086 - 0.114: 28 0.114 - 0.143: 5 Chirality restraints: 826 Sorted by residual: chirality pdb=" CA TYR D 50 " pdb=" N TYR D 50 " pdb=" C TYR D 50 " pdb=" CB TYR D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 823 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 108 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 109 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 232 " 0.013 2.00e-02 2.50e+03 8.19e-03 1.68e+00 pdb=" CG TRP A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 232 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 232 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 232 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 232 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 95 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.018 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 102 2.69 - 3.24: 5149 3.24 - 3.79: 8376 3.79 - 4.35: 11151 4.35 - 4.90: 18915 Nonbonded interactions: 43693 Sorted by model distance: nonbonded pdb=" OE1 GLN D 91 " pdb=" OG1 THR D 99 " model vdw 2.136 3.040 nonbonded pdb=" O TYR D 50 " pdb=" OH TYR D 92 " model vdw 2.163 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 104 " model vdw 2.211 3.040 nonbonded pdb=" O THR A 234 " pdb=" ND2 ASN A 238 " model vdw 2.243 3.120 nonbonded pdb=" OH TYR D 37 " pdb=" OE1 GLN D 90 " model vdw 2.253 3.040 ... (remaining 43688 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: 3.110 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.004 0.034 5378 Z= 0.170 Angle : 0.512 8.148 7308 Z= 0.266 Chirality : 0.039 0.143 826 Planarity : 0.004 0.051 898 Dihedral : 12.003 89.617 1877 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 7.66 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.34), residues: 640 helix: 1.94 (0.29), residues: 296 sheet: -0.46 (0.47), residues: 125 loop : -0.86 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 232 HIS 0.002 0.000 HIS A1256 PHE 0.014 0.002 PHE A 286 TYR 0.020 0.001 TYR D 50 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.14101 ( 309) hydrogen bonds : angle 6.37994 ( 891) SS BOND : bond 0.00379 ( 3) SS BOND : angle 0.86238 ( 6) covalent geometry : bond 0.00394 ( 5375) covalent geometry : angle 0.51195 ( 7302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.571 Fit side-chains REVERT: A 93 ARG cc_start: 0.6909 (ptp-170) cc_final: 0.6642 (ptp-170) REVERT: A 175 THR cc_start: 0.7514 (p) cc_final: 0.7295 (p) REVERT: A 190 THR cc_start: 0.7286 (p) cc_final: 0.6914 (m) REVERT: D 46 LYS cc_start: 0.8329 (mttt) cc_final: 0.7951 (ttpp) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.1397 time to fit residues: 17.6568 Evaluate side-chains 78 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.197912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162033 restraints weight = 5887.221| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.55 r_work: 0.3408 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5378 Z= 0.136 Angle : 0.530 8.151 7308 Z= 0.275 Chirality : 0.039 0.144 826 Planarity : 0.004 0.051 898 Dihedral : 5.439 83.821 725 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.96 % Allowed : 11.23 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.16 (0.35), residues: 640 helix: 2.30 (0.30), residues: 298 sheet: -0.37 (0.47), residues: 127 loop : -0.68 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.018 0.001 PHE B 46 TYR 0.016 0.001 TYR A1292 ARG 0.004 0.000 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 309) hydrogen bonds : angle 4.74671 ( 891) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.79690 ( 6) covalent geometry : bond 0.00290 ( 5375) covalent geometry : angle 0.52995 ( 7302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.578 Fit side-chains REVERT: D 46 LYS cc_start: 0.8424 (mttt) cc_final: 0.8129 (tttm) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 0.1435 time to fit residues: 18.3347 Evaluate side-chains 81 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 55 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN C 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140079 restraints weight = 5956.559| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3357 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5378 Z= 0.165 Angle : 0.531 9.283 7308 Z= 0.274 Chirality : 0.040 0.151 826 Planarity : 0.004 0.050 898 Dihedral : 5.246 81.905 721 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.14 % Allowed : 12.66 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.99 (0.34), residues: 640 helix: 2.08 (0.30), residues: 300 sheet: -0.33 (0.50), residues: 117 loop : -0.73 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.001 0.001 HIS C 38 PHE 0.016 0.002 PHE A 44 TYR 0.019 0.001 TYR D 50 ARG 0.002 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 309) hydrogen bonds : angle 4.55588 ( 891) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.77697 ( 6) covalent geometry : bond 0.00377 ( 5375) covalent geometry : angle 0.53028 ( 7302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.523 Fit side-chains REVERT: D 46 LYS cc_start: 0.8514 (mttt) cc_final: 0.8147 (tttm) REVERT: D 105 LYS cc_start: 0.7136 (ptmt) cc_final: 0.6581 (ttmm) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1452 time to fit residues: 17.8579 Evaluate side-chains 87 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.0070 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.197990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145890 restraints weight = 6043.448| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.57 r_work: 0.3392 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5378 Z= 0.137 Angle : 0.512 9.249 7308 Z= 0.261 Chirality : 0.039 0.140 826 Planarity : 0.004 0.052 898 Dihedral : 5.215 81.804 721 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.67 % Allowed : 13.01 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.34), residues: 640 helix: 2.20 (0.30), residues: 300 sheet: -0.34 (0.50), residues: 117 loop : -0.71 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.013 0.001 PHE A 286 TYR 0.015 0.001 TYR D 50 ARG 0.004 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 309) hydrogen bonds : angle 4.39357 ( 891) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.70468 ( 6) covalent geometry : bond 0.00308 ( 5375) covalent geometry : angle 0.51160 ( 7302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.937 Fit side-chains REVERT: A 57 MET cc_start: 0.7020 (ptm) cc_final: 0.6785 (ppp) REVERT: A 200 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8218 (m110) REVERT: D 46 LYS cc_start: 0.8469 (mttt) cc_final: 0.8145 (tttm) REVERT: D 105 LYS cc_start: 0.7227 (ptmt) cc_final: 0.6706 (ttmm) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.1442 time to fit residues: 17.1724 Evaluate side-chains 88 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.198750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142291 restraints weight = 5971.818| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.66 r_work: 0.3363 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5378 Z= 0.132 Angle : 0.505 8.609 7308 Z= 0.257 Chirality : 0.039 0.138 826 Planarity : 0.004 0.052 898 Dihedral : 5.194 81.586 721 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 13.55 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.13 (0.34), residues: 640 helix: 2.28 (0.30), residues: 300 sheet: -0.32 (0.50), residues: 117 loop : -0.76 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.025 0.001 PHE A1248 TYR 0.015 0.001 TYR D 50 ARG 0.002 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 309) hydrogen bonds : angle 4.29943 ( 891) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.67306 ( 6) covalent geometry : bond 0.00293 ( 5375) covalent geometry : angle 0.50477 ( 7302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8155 (m110) REVERT: C 70 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8341 (mtp180) REVERT: D 46 LYS cc_start: 0.8466 (mttt) cc_final: 0.8079 (tttm) REVERT: D 105 LYS cc_start: 0.7274 (ptmt) cc_final: 0.6813 (ttmm) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 0.1568 time to fit residues: 20.7482 Evaluate side-chains 93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141160 restraints weight = 5926.990| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3352 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5378 Z= 0.144 Angle : 0.516 8.318 7308 Z= 0.264 Chirality : 0.039 0.134 826 Planarity : 0.004 0.053 898 Dihedral : 5.218 81.804 721 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.21 % Allowed : 13.90 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.34), residues: 640 helix: 2.26 (0.30), residues: 300 sheet: -0.39 (0.49), residues: 117 loop : -0.77 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.013 0.001 PHE A 286 TYR 0.016 0.001 TYR D 50 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 309) hydrogen bonds : angle 4.30663 ( 891) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.68486 ( 6) covalent geometry : bond 0.00329 ( 5375) covalent geometry : angle 0.51574 ( 7302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8154 (m110) REVERT: C 70 ARG cc_start: 0.8664 (mtp180) cc_final: 0.8352 (mtp180) REVERT: D 46 LYS cc_start: 0.8529 (mttt) cc_final: 0.8114 (tttm) REVERT: D 105 LYS cc_start: 0.7265 (ptmt) cc_final: 0.6830 (ttmm) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.1432 time to fit residues: 18.4442 Evaluate side-chains 94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139735 restraints weight = 5898.475| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.68 r_work: 0.3343 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5378 Z= 0.162 Angle : 0.539 9.948 7308 Z= 0.273 Chirality : 0.040 0.148 826 Planarity : 0.004 0.053 898 Dihedral : 5.233 81.516 721 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.57 % Allowed : 13.90 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.04 (0.34), residues: 640 helix: 2.18 (0.30), residues: 300 sheet: -0.41 (0.49), residues: 117 loop : -0.75 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.014 0.002 PHE A 290 TYR 0.019 0.001 TYR D 50 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 309) hydrogen bonds : angle 4.34937 ( 891) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.74854 ( 6) covalent geometry : bond 0.00373 ( 5375) covalent geometry : angle 0.53845 ( 7302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8164 (m110) REVERT: D 46 LYS cc_start: 0.8540 (mttt) cc_final: 0.8104 (tttm) REVERT: D 105 LYS cc_start: 0.7194 (ptmt) cc_final: 0.6874 (ttmm) outliers start: 20 outliers final: 15 residues processed: 92 average time/residue: 0.1321 time to fit residues: 16.9277 Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141857 restraints weight = 6000.799| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.66 r_work: 0.3364 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5378 Z= 0.132 Angle : 0.515 8.378 7308 Z= 0.261 Chirality : 0.039 0.139 826 Planarity : 0.004 0.054 898 Dihedral : 5.218 81.741 721 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 14.44 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.14 (0.34), residues: 640 helix: 2.31 (0.30), residues: 300 sheet: -0.43 (0.51), residues: 111 loop : -0.72 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 232 HIS 0.002 0.000 HIS C 38 PHE 0.023 0.001 PHE A1248 TYR 0.016 0.001 TYR D 50 ARG 0.003 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 309) hydrogen bonds : angle 4.27049 ( 891) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.65307 ( 6) covalent geometry : bond 0.00297 ( 5375) covalent geometry : angle 0.51516 ( 7302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8129 (m110) REVERT: D 46 LYS cc_start: 0.8530 (mttt) cc_final: 0.8281 (mtpp) REVERT: D 105 LYS cc_start: 0.7143 (ptmt) cc_final: 0.6909 (ttmm) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1491 time to fit residues: 18.6287 Evaluate side-chains 91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.196690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139948 restraints weight = 5926.556| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.63 r_work: 0.3354 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5378 Z= 0.167 Angle : 0.537 8.428 7308 Z= 0.274 Chirality : 0.041 0.144 826 Planarity : 0.004 0.053 898 Dihedral : 5.257 81.941 721 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 14.26 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.34), residues: 640 helix: 2.21 (0.30), residues: 300 sheet: -0.42 (0.49), residues: 117 loop : -0.67 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.027 0.002 PHE A1248 TYR 0.019 0.001 TYR D 50 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 309) hydrogen bonds : angle 4.36524 ( 891) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.76635 ( 6) covalent geometry : bond 0.00388 ( 5375) covalent geometry : angle 0.53675 ( 7302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8200 (m110) REVERT: D 46 LYS cc_start: 0.8539 (mttt) cc_final: 0.8299 (mtpp) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 0.1479 time to fit residues: 18.9084 Evaluate side-chains 92 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.199734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143021 restraints weight = 5995.411| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.67 r_work: 0.3383 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5378 Z= 0.120 Angle : 0.507 8.189 7308 Z= 0.258 Chirality : 0.039 0.143 826 Planarity : 0.004 0.054 898 Dihedral : 5.229 81.948 721 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 14.62 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.23 (0.35), residues: 640 helix: 2.38 (0.30), residues: 300 sheet: -0.40 (0.51), residues: 111 loop : -0.67 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.001 0.000 HIS C 38 PHE 0.028 0.002 PHE B 66 TYR 0.013 0.001 TYR D 50 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 309) hydrogen bonds : angle 4.25840 ( 891) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.58537 ( 6) covalent geometry : bond 0.00261 ( 5375) covalent geometry : angle 0.50692 ( 7302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8117 (m110) REVERT: D 5 MET cc_start: 0.8713 (mmm) cc_final: 0.8488 (mmm) REVERT: D 46 LYS cc_start: 0.8517 (mttt) cc_final: 0.8113 (tttm) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1514 time to fit residues: 17.8026 Evaluate side-chains 91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.198292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.163244 restraints weight = 5947.128| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.44 r_work: 0.3419 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5378 Z= 0.135 Angle : 0.520 8.066 7308 Z= 0.264 Chirality : 0.040 0.141 826 Planarity : 0.004 0.054 898 Dihedral : 5.238 82.100 721 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.50 % Allowed : 14.62 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.23 (0.34), residues: 640 helix: 2.39 (0.30), residues: 298 sheet: -0.41 (0.51), residues: 111 loop : -0.65 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.002 0.001 HIS C 38 PHE 0.028 0.002 PHE A1248 TYR 0.015 0.001 TYR D 50 ARG 0.004 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 309) hydrogen bonds : angle 4.26766 ( 891) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.68824 ( 6) covalent geometry : bond 0.00307 ( 5375) covalent geometry : angle 0.52015 ( 7302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.35 seconds wall clock time: 57 minutes 56.22 seconds (3476.22 seconds total)