Starting phenix.real_space_refine on Thu Dec 7 19:25:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/12_2023/8tzs_41768.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 36 5.16 5 C 2594 2.51 5 N 637 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3914 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3914 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain breaks: 2 Time building chain proxies: 2.73, per 1000 atoms: 0.70 Number of scatterers: 3914 At special positions: 0 Unit cell: (86.346, 103.32, 78.228, 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 36 16.00 O 647 8.00 N 637 7.00 C 2594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 179 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.61 Conformation dependent library (CDL) restraints added in 898.0 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 54.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.868A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.043A pdb=" N GLN A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 227 through 258 removed outlier: 3.588A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.630A pdb=" N PHE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.112A pdb=" N GLY A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 322 removed outlier: 3.708A pdb=" N ASP A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 335 through 360 Proline residue: A 341 - end of helix removed outlier: 3.753A pdb=" N VAL A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 413 removed outlier: 3.611A pdb=" N SER A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 456 Processing helix chain 'A' and resid 473 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46 removed outlier: 5.976A pdb=" N ILE A 216 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 119 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET A 110 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 186 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 112 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.991A pdb=" N MET A 134 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A 155 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 136 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS A 153 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 138 " --> pdb=" O MET A 151 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 633 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: 1.09 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1185 1.35 - 1.46: 1036 1.46 - 1.58: 1747 1.58 - 1.70: 2 1.70 - 1.81: 60 Bond restraints: 4030 Sorted by residual: bond pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.390 0.113 3.40e-02 8.65e+02 1.10e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.64e+00 bond pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta sigma weight residual 1.465 1.444 0.020 1.11e-02 8.12e+03 3.36e+00 bond pdb=" CB PRO A 170 " pdb=" CG PRO A 170 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.08e+00 ... (remaining 4025 not shown) Histogram of bond angle deviations from ideal: 93.36 - 101.99: 24 101.99 - 110.62: 1146 110.62 - 119.25: 2164 119.25 - 127.87: 2067 127.87 - 136.50: 56 Bond angle restraints: 5457 Sorted by residual: angle pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 112.00 95.97 16.03 1.40e+00 5.10e-01 1.31e+02 angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 93.36 9.84 1.50e+00 4.44e-01 4.30e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 131.82 -15.52 3.50e+00 8.16e-02 1.97e+01 angle pdb=" CA CYS A 179 " pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " ideal model delta sigma weight residual 114.40 124.10 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 5452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2018 16.01 - 32.02: 233 32.02 - 48.04: 78 48.04 - 64.05: 10 64.05 - 80.06: 5 Dihedral angle restraints: 2344 sinusoidal: 951 harmonic: 1393 Sorted by residual: dihedral pdb=" CA CYS A 179 " pdb=" C CYS A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual -180.00 -131.97 -48.03 0 5.00e+00 4.00e-02 9.23e+01 dihedral pdb=" CA LYS A 161 " pdb=" C LYS A 161 " pdb=" N CYS A 162 " pdb=" CA CYS A 162 " ideal model delta harmonic sigma weight residual 180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA GLU A 178 " pdb=" C GLU A 178 " pdb=" N CYS A 179 " pdb=" CA CYS A 179 " ideal model delta harmonic sigma weight residual 180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 457 0.053 - 0.106: 128 0.106 - 0.158: 8 0.158 - 0.211: 1 0.211 - 0.264: 3 Chirality restraints: 597 Sorted by residual: chirality pdb=" CB ILE A 216 " pdb=" CA ILE A 216 " pdb=" CG1 ILE A 216 " pdb=" CG2 ILE A 216 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS A 179 " pdb=" N CYS A 179 " pdb=" C CYS A 179 " pdb=" CB CYS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" C PRO A 263 " pdb=" CB PRO A 263 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 594 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 169 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 170 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 262 " -0.068 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 263 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 490 " 0.010 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 490 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 490 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 490 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 490 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 490 " 0.001 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 155 2.72 - 3.26: 4179 3.26 - 3.81: 6425 3.81 - 4.35: 7251 4.35 - 4.90: 12405 Nonbonded interactions: 30415 Sorted by model distance: nonbonded pdb=" OD1 ASN A 8 " pdb=" OG SER A 495 " model vdw 2.170 2.440 nonbonded pdb=" NH1 ARG A 158 " pdb=" O PRO A 183 " model vdw 2.171 2.520 nonbonded pdb=" O MET A 9 " pdb=" NH2 ARG A 431 " model vdw 2.174 2.520 nonbonded pdb=" O THR A 371 " pdb=" N GLY A 374 " model vdw 2.234 2.520 nonbonded pdb=" O GLN A 326 " pdb=" NH1 ARG A 329 " model vdw 2.289 2.520 ... (remaining 30410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.020 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: 4.600 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.570 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.175 4030 Z= 0.323 Angle : 0.871 16.031 5457 Z= 0.477 Chirality : 0.047 0.264 597 Planarity : 0.007 0.103 672 Dihedral : 15.830 80.062 1436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.24 % Allowed : 20.57 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: 0.65 (0.38), residues: 474 helix: 1.37 (0.32), residues: 223 sheet: 0.18 (0.61), residues: 67 loop : -0.56 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 66 HIS 0.004 0.001 HIS A 192 PHE 0.026 0.002 PHE A 490 TYR 0.016 0.002 TYR A 45 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.475 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1345 time to fit residues: 17.0470 Evaluate side-chains 92 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4030 Z= 0.236 Angle : 0.639 10.474 5457 Z= 0.334 Chirality : 0.044 0.256 597 Planarity : 0.005 0.061 672 Dihedral : 5.408 39.440 511 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.78 % Allowed : 17.73 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.82 (0.39), residues: 474 helix: 1.60 (0.33), residues: 222 sheet: -0.15 (0.57), residues: 77 loop : -0.43 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.004 0.001 HIS A 192 PHE 0.016 0.002 PHE A 401 TYR 0.013 0.002 TYR A 45 ARG 0.003 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.1277 time to fit residues: 17.8211 Evaluate side-chains 107 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0434 time to fit residues: 1.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 0.0970 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4030 Z= 0.171 Angle : 0.600 12.391 5457 Z= 0.305 Chirality : 0.042 0.199 597 Planarity : 0.004 0.047 672 Dihedral : 4.979 37.080 511 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.89 % Allowed : 18.44 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 474 helix: 1.74 (0.33), residues: 229 sheet: 0.68 (0.59), residues: 65 loop : -0.22 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 192 PHE 0.015 0.001 PHE A 318 TYR 0.018 0.001 TYR A 45 ARG 0.001 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.1252 time to fit residues: 17.2915 Evaluate side-chains 95 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0416 time to fit residues: 1.0984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4030 Z= 0.221 Angle : 0.610 12.244 5457 Z= 0.308 Chirality : 0.042 0.134 597 Planarity : 0.004 0.037 672 Dihedral : 4.883 31.867 511 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.07 % Allowed : 21.75 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.39), residues: 474 helix: 1.93 (0.33), residues: 227 sheet: 0.64 (0.63), residues: 63 loop : -0.38 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 66 HIS 0.003 0.001 HIS A 192 PHE 0.021 0.002 PHE A 490 TYR 0.010 0.002 TYR A 140 ARG 0.001 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.1156 time to fit residues: 15.6740 Evaluate side-chains 99 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0660 time to fit residues: 1.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4030 Z= 0.207 Angle : 0.617 13.519 5457 Z= 0.307 Chirality : 0.041 0.130 597 Planarity : 0.004 0.031 672 Dihedral : 4.802 28.482 511 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.13 % Allowed : 22.46 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.39), residues: 474 helix: 1.98 (0.33), residues: 230 sheet: 0.84 (0.64), residues: 54 loop : -0.34 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 66 HIS 0.002 0.001 HIS A 327 PHE 0.034 0.002 PHE A 432 TYR 0.027 0.002 TYR A 140 ARG 0.001 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.1407 time to fit residues: 20.2838 Evaluate side-chains 103 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0481 time to fit residues: 0.9586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4030 Z= 0.172 Angle : 0.626 13.729 5457 Z= 0.309 Chirality : 0.042 0.158 597 Planarity : 0.004 0.032 672 Dihedral : 4.640 26.702 511 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.18 % Allowed : 25.06 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.39), residues: 474 helix: 1.98 (0.33), residues: 229 sheet: 0.53 (0.63), residues: 59 loop : -0.11 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.004 0.001 HIS A 192 PHE 0.020 0.002 PHE A 490 TYR 0.012 0.001 TYR A 45 ARG 0.008 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 0.1286 time to fit residues: 18.0601 Evaluate side-chains 105 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0476 time to fit residues: 0.8699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4030 Z= 0.193 Angle : 0.620 14.715 5457 Z= 0.306 Chirality : 0.042 0.146 597 Planarity : 0.004 0.049 672 Dihedral : 4.610 25.509 511 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.13 % Allowed : 24.11 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.39), residues: 474 helix: 2.00 (0.33), residues: 230 sheet: 0.72 (0.62), residues: 61 loop : -0.30 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.003 0.001 HIS A 192 PHE 0.026 0.002 PHE A 432 TYR 0.012 0.001 TYR A 45 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.1330 time to fit residues: 18.0668 Evaluate side-chains 105 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0423 time to fit residues: 1.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4030 Z= 0.170 Angle : 0.607 14.422 5457 Z= 0.301 Chirality : 0.042 0.148 597 Planarity : 0.004 0.043 672 Dihedral : 4.540 24.142 511 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.42 % Allowed : 24.82 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.39), residues: 474 helix: 2.00 (0.33), residues: 230 sheet: 0.73 (0.62), residues: 61 loop : -0.31 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 66 HIS 0.004 0.001 HIS A 192 PHE 0.020 0.002 PHE A 432 TYR 0.013 0.001 TYR A 45 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.445 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.1344 time to fit residues: 19.3068 Evaluate side-chains 106 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0407 time to fit residues: 0.8607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4030 Z= 0.191 Angle : 0.639 15.012 5457 Z= 0.320 Chirality : 0.043 0.175 597 Planarity : 0.004 0.038 672 Dihedral : 4.562 23.297 511 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.42 % Allowed : 26.48 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 474 helix: 1.94 (0.33), residues: 230 sheet: 0.44 (0.56), residues: 75 loop : -0.22 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.003 0.001 HIS A 192 PHE 0.018 0.002 PHE A 490 TYR 0.013 0.001 TYR A 45 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 110 average time/residue: 0.1437 time to fit residues: 20.0732 Evaluate side-chains 106 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0469 time to fit residues: 0.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.216 Angle : 0.668 14.477 5457 Z= 0.334 Chirality : 0.043 0.152 597 Planarity : 0.004 0.043 672 Dihedral : 4.593 23.040 511 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.71 % Allowed : 26.95 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.39), residues: 474 helix: 1.84 (0.33), residues: 230 sheet: 0.77 (0.62), residues: 61 loop : -0.35 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.002 0.001 HIS A 192 PHE 0.020 0.002 PHE A 432 TYR 0.014 0.002 TYR A 140 ARG 0.003 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.1434 time to fit residues: 19.1346 Evaluate side-chains 105 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0409 time to fit residues: 0.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128964 restraints weight = 8397.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132199 restraints weight = 4898.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134490 restraints weight = 3468.318| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4030 Z= 0.207 Angle : 0.680 14.974 5457 Z= 0.340 Chirality : 0.043 0.181 597 Planarity : 0.004 0.041 672 Dihedral : 4.572 22.267 511 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.47 % Allowed : 27.90 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.39), residues: 474 helix: 1.86 (0.33), residues: 230 sheet: 0.55 (0.55), residues: 75 loop : -0.25 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.002 0.001 HIS A 192 PHE 0.020 0.002 PHE A 490 TYR 0.020 0.002 TYR A 392 ARG 0.003 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.24 seconds wall clock time: 23 minutes 5.54 seconds (1385.54 seconds total)