Starting phenix.real_space_refine on Thu Mar 6 01:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkm_27490/03_2025/8dkm_27490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkm_27490/03_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_27490/03_2025/8dkm_27490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkm_27490/03_2025/8dkm_27490.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkm_27490/03_2025/8dkm_27490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkm_27490/03_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-5624/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: 3.49, per 1000 atoms: 0.80 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: 1.10 Conformation dependent library (CDL) restraints added in 523.2 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: 0.49 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: 1.16 Time building geometry restraints manager: 1.27 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: 1.900 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 4502 Z= 0.217 Angle : 0.673 7.461 6138 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 *********************** 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 : 0.424 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: 0.1364 time to fit residues: 15.0041 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 : 0.457 ------------------------------------------------------------------------------- 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: 0.7980 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: 3.09 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 4502 Z= 0.175 Angle : 0.570 6.798 6138 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 *********************** 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 : 0.432 Fit side-chains REVERT: A 34 MET cc_start: 0.9229 (mmm) cc_final: 0.8740 (mmm) REVERT: P 148 MET cc_start: 0.8572 (tmm) cc_final: 0.8155 (tmm) REVERT: P 287 MET cc_start: 0.7901 (ttm) cc_final: 0.7444 (ttp) REVERT: P 290 TYR cc_start: 0.7737 (t80) cc_final: 0.7450 (t80) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1360 time to fit residues: 14.8123 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 : 0.433 ------------------------------------------------------------------------------- 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: 0.0030 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.154262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124649 restraints weight = 5543.871| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.14 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: 0.8257 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4502 Z= 0.192 Angle : 0.551 6.733 6138 Z= 0.282 Chirality : 0.043 0.226 695 Planarity : 0.004 0.036 767 Dihedral : 5.717 64.612 613 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.49 % Allowed : 13.28 % Favored : 84.23 % 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: -0.40 (0.38), residues: 547 helix: 1.56 (0.37), residues: 205 sheet: -0.55 (0.49), residues: 131 loop : -1.94 (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 *********************** 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 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.449 Fit side-chains REVERT: B 61 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7434 (mtm180) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.1356 time to fit residues: 13.9128 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.151730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122154 restraints weight = 5561.351| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.12 r_work: 0.3127 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.004 0.041 4502 Z= 0.240 Angle : 0.573 7.239 6138 Z= 0.296 Chirality : 0.044 0.154 695 Planarity : 0.004 0.034 767 Dihedral : 5.751 62.446 613 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.15 % Allowed : 13.28 % 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: -0.34 (0.38), residues: 547 helix: 1.71 (0.38), residues: 205 sheet: -0.58 (0.49), residues: 131 loop : -1.98 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.025 0.001 PHE P 289 TYR 0.019 0.002 TYR P 134 ARG 0.005 0.000 ARG B 24 *********************** 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 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.443 Fit side-chains REVERT: B 61 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7474 (mtp180) REVERT: P 148 MET cc_start: 0.8517 (tmm) cc_final: 0.8260 (tmm) outliers start: 20 outliers final: 16 residues processed: 84 average time/residue: 0.1302 time to fit residues: 14.7259 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 : 0.467 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.150527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120518 restraints weight = 5703.848| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.16 r_work: 0.3142 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4502 Z= 0.276 Angle : 0.597 7.779 6138 Z= 0.307 Chirality : 0.044 0.154 695 Planarity : 0.004 0.032 767 Dihedral : 5.867 61.100 613 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.15 % Allowed : 14.11 % Favored : 81.74 % 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: -0.30 (0.38), residues: 547 helix: 1.97 (0.38), residues: 198 sheet: -0.70 (0.49), residues: 133 loop : -2.00 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.013 0.001 PHE P 87 TYR 0.020 0.002 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** 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 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.477 Fit side-chains REVERT: B 61 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7549 (mtp180) outliers start: 20 outliers final: 17 residues processed: 80 average time/residue: 0.1357 time to fit residues: 14.5266 Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122023 restraints weight = 5471.647| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4502 Z= 0.225 Angle : 0.578 7.375 6138 Z= 0.298 Chirality : 0.043 0.150 695 Planarity : 0.004 0.032 767 Dihedral : 5.807 60.180 613 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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: -0.31 (0.38), residues: 547 helix: 1.96 (0.38), residues: 199 sheet: -0.89 (0.48), residues: 141 loop : -1.88 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.026 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.006 0.000 ARG B 24 *********************** 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 89 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.431 Fit side-chains REVERT: A 18 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8615 (tt) REVERT: P 148 MET cc_start: 0.8572 (tmm) cc_final: 0.8337 (tmm) outliers start: 17 outliers final: 15 residues processed: 78 average time/residue: 0.1201 time to fit residues: 12.9035 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.151936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122174 restraints weight = 5532.163| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.13 r_work: 0.3144 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4502 Z= 0.222 Angle : 0.576 7.236 6138 Z= 0.296 Chirality : 0.043 0.150 695 Planarity : 0.004 0.032 767 Dihedral : 5.777 58.960 613 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 : 3.94 % Allowed : 15.98 % 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: -0.23 (0.39), residues: 547 helix: 2.01 (0.38), residues: 199 sheet: -0.85 (0.48), residues: 141 loop : -1.81 (0.43), residues: 207 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 0.023 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 *********************** 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: 19 poor density : 70 time to evaluate : 0.433 Fit side-chains REVERT: A 18 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8542 (tt) REVERT: B 82 ASP cc_start: 0.8028 (m-30) cc_final: 0.7826 (m-30) outliers start: 19 outliers final: 16 residues processed: 77 average time/residue: 0.1177 time to fit residues: 12.6622 Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 25 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.153808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124013 restraints weight = 5506.159| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.13 r_work: 0.3172 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4502 Z= 0.177 Angle : 0.549 6.860 6138 Z= 0.282 Chirality : 0.042 0.145 695 Planarity : 0.004 0.032 767 Dihedral : 5.654 57.802 613 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -0.12 (0.39), residues: 547 helix: 2.06 (0.38), residues: 199 sheet: -0.77 (0.48), residues: 141 loop : -1.73 (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 0.020 0.001 PHE P 289 TYR 0.017 0.001 TYR P 134 ARG 0.008 0.000 ARG B 24 *********************** 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 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.417 Fit side-chains REVERT: A 18 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 82 ASP cc_start: 0.7926 (m-30) cc_final: 0.7712 (m-30) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.0983 time to fit residues: 10.3340 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 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: 1.9990 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: 0.0670 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.152960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123062 restraints weight = 5492.311| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.13 r_work: 0.3157 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4502 Z= 0.209 Angle : 0.575 8.917 6138 Z= 0.291 Chirality : 0.043 0.148 695 Planarity : 0.004 0.031 767 Dihedral : 5.675 57.158 613 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.46 % 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: -0.11 (0.39), residues: 547 helix: 2.03 (0.38), residues: 200 sheet: -0.75 (0.48), residues: 141 loop : -1.70 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.019 0.001 PHE P 289 TYR 0.017 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 *********************** 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 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.479 Fit side-chains REVERT: A 18 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8503 (tt) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.1213 time to fit residues: 12.5375 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.151486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121748 restraints weight = 5474.310| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.11 r_work: 0.3139 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4502 Z= 0.240 Angle : 0.571 6.423 6138 Z= 0.295 Chirality : 0.043 0.152 695 Planarity : 0.004 0.031 767 Dihedral : 5.755 57.345 613 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.32 % Allowed : 17.22 % Favored : 79.46 % 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: -0.07 (0.39), residues: 547 helix: 2.13 (0.38), residues: 200 sheet: -0.76 (0.48), residues: 141 loop : -1.73 (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 0.019 0.001 PHE P 289 TYR 0.018 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 ********************** 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 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.479 Fit side-chains REVERT: A 18 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8581 (tt) outliers start: 16 outliers final: 14 residues processed: 74 average time/residue: 0.1120 time to fit residues: 11.5838 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 344 VAL 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: 5.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 11 optimal weight: 0.0060 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.155266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125535 restraints weight = 5519.619| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.14 r_work: 0.3213 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4502 Z= 0.156 Angle : 0.535 5.501 6138 Z= 0.276 Chirality : 0.042 0.142 695 Planarity : 0.004 0.032 767 Dihedral : 5.546 56.830 613 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.28 % Allowed : 18.26 % Favored : 79.46 % 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: 0.06 (0.39), residues: 547 helix: 2.30 (0.38), residues: 198 sheet: -0.71 (0.49), residues: 141 loop : -1.68 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.000 0.000 HIS B 55 PHE 0.017 0.001 PHE P 289 TYR 0.014 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3199.30 seconds wall clock time: 56 minutes 56.25 seconds (3416.25 seconds total)