Starting phenix.real_space_refine on Fri Dec 27 11:20:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkm_27490/12_2024/8dkm_27490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkm_27490/12_2024/8dkm_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_27490/12_2024/8dkm_27490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkm_27490/12_2024/8dkm_27490.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkm_27490/12_2024/8dkm_27490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkm_27490/12_2024/8dkm_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-5532/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: 3.71, per 1000 atoms: 0.85 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: 1.09 Conformation dependent library (CDL) restraints added in 528.0 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: 0.50 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: 1.20 Time building geometry restraints manager: 1.23 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: 1.670 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: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 : 0.490 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: 0.1436 time to fit residues: 15.9199 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 : 0.454 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.437 Fit side-chains REVERT: A 34 MET cc_start: 0.8861 (mmm) cc_final: 0.8397 (mmm) REVERT: B 81 GLU cc_start: 0.7019 (mp0) cc_final: 0.6773 (mp0) REVERT: P 148 MET cc_start: 0.8598 (tmm) cc_final: 0.8180 (tmm) REVERT: P 287 MET cc_start: 0.7933 (ttm) cc_final: 0.7519 (ttp) REVERT: P 290 TYR cc_start: 0.7506 (t80) cc_final: 0.7263 (t80) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1379 time to fit residues: 15.0156 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 : 0.501 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4502 Z= 0.331 Angle : 0.622 7.999 6138 Z= 0.321 Chirality : 0.046 0.224 695 Planarity : 0.005 0.034 767 Dihedral : 6.069 64.695 613 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.32 % Allowed : 12.66 % Favored : 84.02 % 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: -0.54 (0.38), residues: 547 helix: 1.66 (0.37), residues: 199 sheet: -0.85 (0.48), residues: 135 loop : -2.01 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 182 HIS 0.004 0.001 HIS B 55 PHE 0.014 0.001 PHE P 87 TYR 0.021 0.002 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 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.450 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 61 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7569 (mtp180) REVERT: P 148 MET cc_start: 0.8549 (tmm) cc_final: 0.8343 (tmm) outliers start: 16 outliers final: 15 residues processed: 83 average time/residue: 0.1430 time to fit residues: 15.8745 Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 149 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 149 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1518 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= 0.211 Angle : 0.580 7.493 6138 Z= 0.298 Chirality : 0.043 0.152 695 Planarity : 0.004 0.034 767 Dihedral : 5.872 63.741 613 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.94 % Allowed : 14.73 % Favored : 81.33 % 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: -0.35 (0.38), residues: 547 helix: 1.84 (0.37), residues: 199 sheet: -0.70 (0.49), residues: 133 loop : -1.96 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.023 0.001 PHE P 289 TYR 0.019 0.001 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 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.382 Fit side-chains REVERT: B 61 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7411 (mtp180) REVERT: B 82 ASP cc_start: 0.7650 (m-30) cc_final: 0.7150 (m-30) REVERT: P 148 MET cc_start: 0.8564 (tmm) cc_final: 0.8329 (tmm) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.1337 time to fit residues: 14.4871 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 : 0.525 ------------------------------------------------------------------------------- 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 247 PHE 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 29 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN P 149 ASN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 ASN ** P 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1623 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= 0.190 Angle : 0.562 6.944 6138 Z= 0.287 Chirality : 0.043 0.145 695 Planarity : 0.004 0.033 767 Dihedral : 5.700 60.916 613 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 16.18 % Favored : 80.50 % 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: -0.24 (0.38), residues: 547 helix: 1.97 (0.38), residues: 199 sheet: -0.86 (0.48), residues: 141 loop : -1.79 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.010 0.001 PHE P 345 TYR 0.017 0.001 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 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.488 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1310 time to fit residues: 13.9309 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 247 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4502 Z= 0.220 Angle : 0.563 7.104 6138 Z= 0.290 Chirality : 0.043 0.148 695 Planarity : 0.004 0.032 767 Dihedral : 5.718 59.935 613 Min Nonbonded Distance : 2.593 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: -0.24 (0.39), residues: 547 helix: 2.00 (0.38), residues: 199 sheet: -0.89 (0.48), residues: 141 loop : -1.78 (0.43), residues: 207 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 0.018 0.001 TYR P 134 ARG 0.007 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 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.485 Fit side-chains REVERT: A 18 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 17 outliers final: 15 residues processed: 77 average time/residue: 0.1195 time to fit residues: 12.7112 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 217 LEU 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 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN P 149 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4502 Z= 0.183 Angle : 0.554 6.759 6138 Z= 0.285 Chirality : 0.042 0.143 695 Planarity : 0.004 0.032 767 Dihedral : 5.648 58.442 613 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.73 % Allowed : 15.56 % 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: -0.22 (0.38), residues: 547 helix: 1.83 (0.38), residues: 205 sheet: -0.75 (0.48), residues: 139 loop : -1.78 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.028 0.001 PHE P 289 TYR 0.017 0.001 TYR P 134 ARG 0.007 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: 18 poor density : 71 time to evaluate : 0.428 Fit side-chains REVERT: A 18 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8405 (tt) REVERT: P 148 MET cc_start: 0.8530 (tmm) cc_final: 0.8278 (tmm) outliers start: 18 outliers final: 16 residues processed: 79 average time/residue: 0.1196 time to fit residues: 13.1038 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN P 149 ASN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1808 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= 0.214 Angle : 0.569 8.666 6138 Z= 0.290 Chirality : 0.043 0.147 695 Planarity : 0.004 0.031 767 Dihedral : 5.681 57.708 613 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.73 % Allowed : 16.39 % Favored : 79.88 % 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: 1.79 (0.38), residues: 205 sheet: -0.69 (0.48), residues: 139 loop : -1.76 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.002 0.000 HIS B 55 PHE 0.024 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 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.468 Fit side-chains REVERT: A 18 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8434 (tt) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.1154 time to fit residues: 12.3798 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 : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 217 LEU 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 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4502 Z= 0.244 Angle : 0.574 6.514 6138 Z= 0.298 Chirality : 0.044 0.151 695 Planarity : 0.004 0.031 767 Dihedral : 5.767 57.567 613 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 17.43 % Favored : 79.25 % 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: 2.11 (0.38), residues: 199 sheet: -0.79 (0.47), residues: 141 loop : -1.76 (0.44), residues: 207 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 0.022 0.001 PHE P 289 TYR 0.019 0.001 TYR P 134 ARG 0.008 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 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.460 Fit side-chains REVERT: A 18 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8463 (tt) REVERT: P 286 TYR cc_start: 0.7377 (t80) cc_final: 0.7165 (t80) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1143 time to fit residues: 12.2932 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 : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 217 LEU 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 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 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 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4502 Z= 0.217 Angle : 0.571 6.183 6138 Z= 0.294 Chirality : 0.043 0.148 695 Planarity : 0.004 0.031 767 Dihedral : 5.720 57.244 613 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 17.63 % Favored : 79.05 % 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: 1.90 (0.38), residues: 206 sheet: -0.68 (0.48), residues: 139 loop : -1.77 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.022 0.001 PHE P 289 TYR 0.017 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 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.459 Fit side-chains REVERT: A 18 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 16 outliers final: 15 residues processed: 71 average time/residue: 0.1247 time to fit residues: 12.6401 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 217 LEU 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 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123546 restraints weight = 5444.003| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.11 r_work: 0.3146 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4502 Z= 0.193 Angle : 0.551 5.863 6138 Z= 0.286 Chirality : 0.042 0.145 695 Planarity : 0.004 0.031 767 Dihedral : 5.650 56.941 613 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.53 % Allowed : 17.43 % Favored : 79.05 % 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: 2.00 (0.38), residues: 205 sheet: -0.67 (0.48), residues: 139 loop : -1.76 (0.44), residues: 203 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 0.021 0.001 PHE P 289 TYR 0.016 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: 1277.92 seconds wall clock time: 24 minutes 9.55 seconds (1449.55 seconds total)