Starting phenix.real_space_refine on Sat May 10 00:31:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkm_27490/05_2025/8dkm_27490.cif" } resolution = 3.39 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= 0.004 sd= 0.074 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 17 5.16 5 C 2867 2.51 5 N 706 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4383 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IYY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.74 Number of scatterers: 4383 At special positions: 0 Unit cell: (85.884, 105.25, 106.092, 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 17 16.00 O 793 8.00 N 706 7.00 C 2867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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: 1.05 Conformation dependent library (CDL) restraints added in 493.6 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 8 sheets defined 38.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.936A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.939A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 141 removed outlier: 3.651A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.651A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 234 through 257 removed outlier: 3.620A pdb=" N VAL P 257 " --> pdb=" O ILE P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 removed outlier: 3.542A pdb=" N PHE P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.725A pdb=" N VAL P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.632A pdb=" N PHE P 336 " --> pdb=" O ASP P 332 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.973A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.420A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.435A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 removed outlier: 3.595A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.589A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU P 101 " --> pdb=" O GLY P 110 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG P 112 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL P 99 " --> pdb=" O ARG P 112 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR P 57 " --> pdb=" O HIS P 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.589A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 621 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: 1.08 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1570 1.38 - 1.56: 2907 1.56 - 1.74: 0 1.74 - 1.92: 24 1.92 - 2.10: 1 Bond restraints: 4502 Sorted by residual: bond pdb=" C ASN P 301 " pdb=" O ASN P 301 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.88e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" CA VAL P 302 " pdb=" CB VAL P 302 " ideal model delta sigma weight residual 1.540 1.501 0.038 1.37e-02 5.33e+03 7.81e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.42e-02 4.96e+03 5.60e+00 ... (remaining 4497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 5916 1.49 - 2.98: 158 2.98 - 4.48: 44 4.48 - 5.97: 12 5.97 - 7.46: 8 Bond angle restraints: 6138 Sorted by residual: angle pdb=" N GLY P 300 " pdb=" CA GLY P 300 " pdb=" C GLY P 300 " ideal model delta sigma weight residual 113.37 105.91 7.46 1.34e+00 5.57e-01 3.10e+01 angle pdb=" N TYR P 271 " pdb=" CA TYR P 271 " pdb=" C TYR P 271 " ideal model delta sigma weight residual 111.36 115.75 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N VAL P 259 " pdb=" CA VAL P 259 " pdb=" C VAL P 259 " ideal model delta sigma weight residual 111.45 107.73 3.72 9.30e-01 1.16e+00 1.60e+01 angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.82 118.01 3.81 1.21e+00 6.83e-01 9.94e+00 ... (remaining 6133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 2277 15.19 - 30.38: 250 30.38 - 45.57: 53 45.57 - 60.76: 8 60.76 - 75.94: 8 Dihedral angle restraints: 2596 sinusoidal: 999 harmonic: 1597 Sorted by residual: dihedral pdb=" CA SER P 270 " pdb=" C SER P 270 " pdb=" N TYR P 271 " pdb=" CA TYR P 271 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.96 31.04 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 549 0.050 - 0.100: 116 0.100 - 0.150: 26 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" CA TYR P 271 " pdb=" N TYR P 271 " pdb=" C TYR P 271 " pdb=" CB TYR P 271 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL P 259 " pdb=" N VAL P 259 " pdb=" C VAL P 259 " pdb=" CB VAL P 259 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 692 not shown) Planarity restraints: 767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN P 199 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO P 200 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO P 200 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 200 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " -0.014 2.00e-02 2.50e+03 1.10e-02 3.02e+00 pdb=" CG TRP P 182 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO P 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 764 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 797 2.77 - 3.30: 4104 3.30 - 3.84: 7025 3.84 - 4.37: 7958 4.37 - 4.90: 14353 Nonbonded interactions: 34237 Sorted by model distance: nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.245 3.040 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 73 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP B 42 " pdb=" N ILE B 43 " model vdw 2.277 3.120 nonbonded pdb=" OD1 ASP P 161 " pdb=" N PHE P 162 " model vdw 2.285 3.120 ... (remaining 34232 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.870 Find NCS groups from input model: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.003 0.039 4504 Z= 0.196 Angle : 0.673 7.461 6142 Z= 0.357 Chirality : 0.045 0.250 695 Planarity : 0.005 0.068 767 Dihedral : 13.474 75.945 1570 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 0.41 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.94 (0.37), residues: 547 helix: 1.16 (0.39), residues: 198 sheet: -0.77 (0.48), residues: 131 loop : -2.24 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 182 HIS 0.002 0.001 HIS P 211 PHE 0.017 0.001 PHE P 289 TYR 0.015 0.001 TYR P 286 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.14622 ( 219) hydrogen bonds : angle 6.33353 ( 621) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.03537 ( 4) covalent geometry : bond 0.00344 ( 4502) covalent geometry : angle 0.67308 ( 6138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.483 Fit side-chains REVERT: A 83 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7269 (tp-100) REVERT: B 81 GLU cc_start: 0.7038 (mp0) cc_final: 0.6829 (mp0) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.1383 time to fit residues: 15.1375 Evaluate side-chains 70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 27 GLN P 149 ASN ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.155131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125479 restraints weight = 5499.368| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.16 r_work: 0.3192 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.120 Angle : 0.570 6.798 6142 Z= 0.290 Chirality : 0.043 0.142 695 Planarity : 0.004 0.045 767 Dihedral : 6.203 66.467 618 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.66 % Allowed : 10.17 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 547 helix: 1.33 (0.37), residues: 205 sheet: -0.50 (0.49), residues: 127 loop : -2.06 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.022 0.001 PHE P 289 TYR 0.020 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 219) hydrogen bonds : angle 4.59769 ( 621) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.88263 ( 4) covalent geometry : bond 0.00272 ( 4502) covalent geometry : angle 0.57006 ( 6138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.462 Fit side-chains REVERT: A 34 MET cc_start: 0.9229 (mmm) cc_final: 0.8740 (mmm) REVERT: P 148 MET cc_start: 0.8571 (tmm) cc_final: 0.8155 (tmm) REVERT: P 287 MET cc_start: 0.7900 (ttm) cc_final: 0.7443 (ttp) REVERT: P 290 TYR cc_start: 0.7738 (t80) cc_final: 0.7450 (t80) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1336 time to fit residues: 14.5044 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.154425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124813 restraints weight = 5540.384| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.14 r_work: 0.3183 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.124 Angle : 0.549 6.671 6142 Z= 0.282 Chirality : 0.043 0.216 695 Planarity : 0.004 0.036 767 Dihedral : 5.698 64.613 613 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.28 % Allowed : 13.28 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.38), residues: 547 helix: 1.55 (0.37), residues: 205 sheet: -0.55 (0.49), residues: 131 loop : -1.93 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 182 HIS 0.002 0.000 HIS B 55 PHE 0.009 0.001 PHE P 345 TYR 0.019 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 219) hydrogen bonds : angle 4.38845 ( 621) SS BOND : bond 0.00461 ( 2) SS BOND : angle 1.14556 ( 4) covalent geometry : bond 0.00290 ( 4502) covalent geometry : angle 0.54829 ( 6138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.495 Fit side-chains REVERT: B 61 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7464 (mtm180) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.1380 time to fit residues: 14.2438 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122621 restraints weight = 5557.453| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.15 r_work: 0.3171 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4504 Z= 0.146 Angle : 0.564 7.036 6142 Z= 0.291 Chirality : 0.043 0.153 695 Planarity : 0.004 0.034 767 Dihedral : 5.703 62.437 613 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.94 % Allowed : 13.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.38), residues: 547 helix: 1.71 (0.37), residues: 205 sheet: -0.56 (0.49), residues: 131 loop : -1.95 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.025 0.001 PHE P 289 TYR 0.019 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 219) hydrogen bonds : angle 4.30191 ( 621) SS BOND : bond 0.00441 ( 2) SS BOND : angle 0.94724 ( 4) covalent geometry : bond 0.00350 ( 4502) covalent geometry : angle 0.56398 ( 6138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.489 Fit side-chains REVERT: B 61 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7518 (mtp180) REVERT: P 148 MET cc_start: 0.8489 (tmm) cc_final: 0.8212 (tmm) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.1301 time to fit residues: 14.3055 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122485 restraints weight = 5669.642| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.11 r_work: 0.3149 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4504 Z= 0.147 Angle : 0.572 7.186 6142 Z= 0.293 Chirality : 0.043 0.148 695 Planarity : 0.004 0.032 767 Dihedral : 5.725 60.801 613 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.73 % Allowed : 14.32 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.22 (0.38), residues: 547 helix: 1.96 (0.38), residues: 199 sheet: -0.66 (0.49), residues: 133 loop : -1.86 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.011 0.001 PHE P 87 TYR 0.018 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 219) hydrogen bonds : angle 4.24442 ( 621) SS BOND : bond 0.00427 ( 2) SS BOND : angle 0.86055 ( 4) covalent geometry : bond 0.00356 ( 4502) covalent geometry : angle 0.57143 ( 6138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.535 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 82 average time/residue: 0.1328 time to fit residues: 14.5258 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN P 222 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122782 restraints weight = 5470.464| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.11 r_work: 0.3155 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4504 Z= 0.140 Angle : 0.572 7.018 6142 Z= 0.293 Chirality : 0.043 0.148 695 Planarity : 0.004 0.031 767 Dihedral : 5.725 59.476 613 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.53 % Allowed : 15.77 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.27 (0.38), residues: 547 helix: 2.01 (0.38), residues: 198 sheet: -0.88 (0.48), residues: 141 loop : -1.86 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.027 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 219) hydrogen bonds : angle 4.17465 ( 621) SS BOND : bond 0.00419 ( 2) SS BOND : angle 2.86840 ( 4) covalent geometry : bond 0.00336 ( 4502) covalent geometry : angle 0.56706 ( 6138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.501 Fit side-chains REVERT: P 148 MET cc_start: 0.8563 (tmm) cc_final: 0.8326 (tmm) outliers start: 17 outliers final: 16 residues processed: 77 average time/residue: 0.1187 time to fit residues: 12.6260 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122753 restraints weight = 5554.215| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3150 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4504 Z= 0.140 Angle : 0.575 6.976 6142 Z= 0.296 Chirality : 0.043 0.149 695 Planarity : 0.004 0.031 767 Dihedral : 5.713 58.408 613 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.15 % Allowed : 15.56 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.38), residues: 547 helix: 2.05 (0.38), residues: 198 sheet: -0.81 (0.48), residues: 141 loop : -1.83 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.022 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 219) hydrogen bonds : angle 4.13617 ( 621) SS BOND : bond 0.00445 ( 2) SS BOND : angle 3.39015 ( 4) covalent geometry : bond 0.00336 ( 4502) covalent geometry : angle 0.56914 ( 6138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.459 Fit side-chains REVERT: A 18 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8533 (tt) REVERT: P 290 TYR cc_start: 0.7637 (t80) cc_final: 0.7428 (t80) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.1131 time to fit residues: 11.8099 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123583 restraints weight = 5527.356| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.13 r_work: 0.3164 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4504 Z= 0.127 Angle : 0.560 6.833 6142 Z= 0.288 Chirality : 0.043 0.147 695 Planarity : 0.004 0.033 767 Dihedral : 5.659 57.683 613 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 15.98 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.13 (0.39), residues: 547 helix: 2.05 (0.38), residues: 199 sheet: -0.77 (0.48), residues: 141 loop : -1.72 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.020 0.001 PHE P 289 TYR 0.017 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 219) hydrogen bonds : angle 4.07996 ( 621) SS BOND : bond 0.00394 ( 2) SS BOND : angle 2.88875 ( 4) covalent geometry : bond 0.00302 ( 4502) covalent geometry : angle 0.55529 ( 6138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.445 Fit side-chains REVERT: A 18 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8522 (tt) REVERT: P 148 MET cc_start: 0.8518 (tmm) cc_final: 0.8295 (tmm) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1140 time to fit residues: 11.7011 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123596 restraints weight = 5494.611| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.13 r_work: 0.3165 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4504 Z= 0.130 Angle : 0.568 6.756 6142 Z= 0.290 Chirality : 0.043 0.146 695 Planarity : 0.004 0.032 767 Dihedral : 5.645 57.189 613 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.53 % Allowed : 16.18 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.08 (0.39), residues: 547 helix: 2.08 (0.38), residues: 199 sheet: -0.74 (0.48), residues: 141 loop : -1.70 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.011 0.001 PHE P 345 TYR 0.017 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 219) hydrogen bonds : angle 4.07178 ( 621) SS BOND : bond 0.00423 ( 2) SS BOND : angle 3.19091 ( 4) covalent geometry : bond 0.00309 ( 4502) covalent geometry : angle 0.56241 ( 6138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.499 Fit side-chains REVERT: A 18 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8524 (tt) REVERT: P 148 MET cc_start: 0.8518 (tmm) cc_final: 0.8255 (tmm) REVERT: P 290 TYR cc_start: 0.7645 (t80) cc_final: 0.7412 (t80) outliers start: 17 outliers final: 15 residues processed: 72 average time/residue: 0.1149 time to fit residues: 11.6808 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123904 restraints weight = 5487.401| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.13 r_work: 0.3135 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 0.029 4504 Z= 0.124 Angle : 0.555 6.721 6142 Z= 0.285 Chirality : 0.042 0.146 695 Planarity : 0.004 0.031 767 Dihedral : 5.609 56.788 613 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 16.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.39), residues: 547 helix: 2.10 (0.38), residues: 199 sheet: -0.72 (0.49), residues: 141 loop : -1.68 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.011 0.001 PHE P 345 TYR 0.016 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 219) hydrogen bonds : angle 4.04153 ( 621) SS BOND : bond 0.00400 ( 2) SS BOND : angle 3.04799 ( 4) covalent geometry : bond 0.00294 ( 4502) covalent geometry : angle 0.54934 ( 6138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.464 Fit side-chains REVERT: A 18 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8570 (tt) REVERT: P 148 MET cc_start: 0.8560 (tmm) cc_final: 0.8312 (tmm) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.1190 time to fit residues: 12.6408 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122478 restraints weight = 5551.017| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.15 r_work: 0.3150 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4504 Z= 0.144 Angle : 0.581 8.790 6142 Z= 0.296 Chirality : 0.043 0.149 695 Planarity : 0.004 0.033 767 Dihedral : 5.674 56.860 613 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.32 % Allowed : 17.01 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 547 helix: 2.04 (0.38), residues: 200 sheet: -0.75 (0.48), residues: 141 loop : -1.69 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.011 0.001 PHE P 87 TYR 0.020 0.001 TYR P 271 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 219) hydrogen bonds : angle 4.14387 ( 621) SS BOND : bond 0.00458 ( 2) SS BOND : angle 3.12415 ( 4) covalent geometry : bond 0.00350 ( 4502) covalent geometry : angle 0.57610 ( 6138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.98 seconds wall clock time: 42 minutes 18.37 seconds (2538.37 seconds total)