Starting phenix.real_space_refine on Sun Mar 10 18:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/03_2024/8tzs_41768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/03_2024/8tzs_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_41768/03_2024/8tzs_41768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/03_2024/8tzs_41768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/03_2024/8tzs_41768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/03_2024/8tzs_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-dev-5265/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: 2.67, per 1000 atoms: 0.68 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: 1.39 Conformation dependent library (CDL) restraints added in 834.3 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: 0.36 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: 0.99 Time building geometry restraints manager: 1.55 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: 0.920 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: 4.650 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.320 Find NCS groups from input model: 0.100 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- 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 : 0.476 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1318 time to fit residues: 16.7710 Evaluate side-chains 92 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4030 Z= 0.234 Angle : 0.632 10.338 5457 Z= 0.331 Chirality : 0.044 0.252 597 Planarity : 0.005 0.060 672 Dihedral : 5.382 38.347 511 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.02 % Allowed : 17.73 % Favored : 78.25 % 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: 0.89 (0.39), residues: 474 helix: 1.59 (0.33), residues: 223 sheet: -0.04 (0.58), residues: 75 loop : -0.33 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.002 PHE A 401 TYR 0.014 0.002 TYR A 45 ARG 0.003 0.000 ARG A 200 *********************** 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 118 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6139 (t80) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.1296 time to fit residues: 18.1432 Evaluate side-chains 106 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR 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: 10.0000 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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: 0.7618 moved from start: 0.1491 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= 0.184 Angle : 0.606 13.076 5457 Z= 0.306 Chirality : 0.042 0.187 597 Planarity : 0.004 0.044 672 Dihedral : 5.060 37.241 511 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.26 % Allowed : 19.39 % Favored : 76.36 % 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: 1.23 (0.39), residues: 474 helix: 1.79 (0.33), residues: 229 sheet: 0.57 (0.58), residues: 67 loop : -0.31 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 192 PHE 0.018 0.002 PHE A 490 TYR 0.007 0.001 TYR A 335 ARG 0.001 0.000 ARG A 200 *********************** 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 119 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 TYR cc_start: 0.8053 (t80) cc_final: 0.7715 (t80) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1387 time to fit residues: 20.0932 Evaluate side-chains 109 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4030 Z= 0.245 Angle : 0.621 12.400 5457 Z= 0.316 Chirality : 0.042 0.139 597 Planarity : 0.004 0.036 672 Dihedral : 5.027 33.660 511 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.15 % Allowed : 19.86 % Favored : 74.00 % 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: 1.29 (0.39), residues: 474 helix: 1.90 (0.33), residues: 227 sheet: 0.35 (0.56), residues: 76 loop : -0.28 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 496 PHE 0.020 0.002 PHE A 490 TYR 0.024 0.002 TYR A 140 ARG 0.001 0.000 ARG A 255 *********************** 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 125 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8535 (pt) REVERT: A 432 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 478 TYR cc_start: 0.8126 (t80) cc_final: 0.7803 (t80) REVERT: A 489 MET cc_start: 0.8842 (mtm) cc_final: 0.8562 (mtm) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.1272 time to fit residues: 18.7700 Evaluate side-chains 114 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.2122 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= 0.190 Angle : 0.612 13.973 5457 Z= 0.303 Chirality : 0.042 0.158 597 Planarity : 0.004 0.034 672 Dihedral : 4.805 28.990 511 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.44 % Allowed : 20.80 % 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: 1.40 (0.39), residues: 474 helix: 1.99 (0.33), residues: 229 sheet: 0.75 (0.59), residues: 63 loop : -0.35 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 66 HIS 0.003 0.001 HIS A 192 PHE 0.014 0.002 PHE A 318 TYR 0.008 0.001 TYR A 492 ARG 0.001 0.000 ARG A 431 *********************** 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 126 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 478 TYR cc_start: 0.8123 (t80) cc_final: 0.7820 (t80) outliers start: 23 outliers final: 19 residues processed: 116 average time/residue: 0.1273 time to fit residues: 19.0019 Evaluate side-chains 116 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL 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: 0.6980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 26 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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: 0.7600 moved from start: 0.2525 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= 0.163 Angle : 0.613 13.644 5457 Z= 0.304 Chirality : 0.041 0.153 597 Planarity : 0.004 0.031 672 Dihedral : 4.604 27.073 511 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.67 % Allowed : 21.99 % 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: 1.47 (0.39), residues: 474 helix: 2.00 (0.33), residues: 230 sheet: 0.74 (0.63), residues: 61 loop : -0.21 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 148 HIS 0.003 0.001 HIS A 57 PHE 0.030 0.002 PHE A 490 TYR 0.009 0.001 TYR A 492 ARG 0.007 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 129 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8309 (m-10) cc_final: 0.8106 (m-10) REVERT: A 98 LEU cc_start: 0.8379 (mm) cc_final: 0.8146 (mm) REVERT: A 101 MET cc_start: 0.8101 (ptp) cc_final: 0.7607 (pmm) REVERT: A 219 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 354 MET cc_start: 0.8035 (mtm) cc_final: 0.7811 (mtp) REVERT: A 432 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6171 (t80) REVERT: A 478 TYR cc_start: 0.8114 (t80) cc_final: 0.7823 (t80) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.1244 time to fit residues: 19.0506 Evaluate side-chains 119 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.2663 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= 0.162 Angle : 0.610 14.342 5457 Z= 0.300 Chirality : 0.041 0.146 597 Planarity : 0.004 0.046 672 Dihedral : 4.530 24.979 511 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.73 % Allowed : 23.17 % 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: 1.60 (0.39), residues: 474 helix: 2.10 (0.33), residues: 230 sheet: 0.83 (0.62), residues: 61 loop : -0.17 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 66 HIS 0.002 0.001 HIS A 496 PHE 0.019 0.001 PHE A 490 TYR 0.031 0.001 TYR A 140 ARG 0.004 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 126 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8386 (mm) cc_final: 0.8057 (mm) REVERT: A 101 MET cc_start: 0.8142 (ptp) cc_final: 0.7564 (pmm) REVERT: A 150 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 432 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6212 (t80) REVERT: A 478 TYR cc_start: 0.8125 (t80) cc_final: 0.7828 (t80) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.1377 time to fit residues: 20.3574 Evaluate side-chains 118 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 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 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4030 Z= 0.206 Angle : 0.635 15.036 5457 Z= 0.315 Chirality : 0.042 0.177 597 Planarity : 0.004 0.044 672 Dihedral : 4.635 24.782 511 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.20 % Allowed : 23.88 % Favored : 70.92 % 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: 1.54 (0.39), residues: 474 helix: 1.99 (0.33), residues: 231 sheet: 0.75 (0.62), residues: 61 loop : -0.10 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.026 0.002 PHE A 490 TYR 0.013 0.001 TYR A 140 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 122 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 104 SER cc_start: 0.8829 (p) cc_final: 0.8490 (p) REVERT: A 219 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8502 (pt) REVERT: A 478 TYR cc_start: 0.8182 (t80) cc_final: 0.7800 (t80) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.1343 time to fit residues: 19.2693 Evaluate side-chains 119 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4030 Z= 0.207 Angle : 0.647 15.386 5457 Z= 0.318 Chirality : 0.042 0.165 597 Planarity : 0.004 0.044 672 Dihedral : 4.741 25.427 511 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.73 % Allowed : 24.59 % Favored : 70.69 % 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: 1.55 (0.39), residues: 474 helix: 2.02 (0.32), residues: 231 sheet: 0.34 (0.55), residues: 75 loop : 0.04 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.022 0.002 PHE A 365 TYR 0.017 0.002 TYR A 140 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 123 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8318 (mm) cc_final: 0.8105 (mm) REVERT: A 101 MET cc_start: 0.8110 (ptp) cc_final: 0.7630 (pmm) REVERT: A 104 SER cc_start: 0.8855 (p) cc_final: 0.8518 (p) REVERT: A 219 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8517 (pt) REVERT: A 310 MET cc_start: 0.8393 (tpt) cc_final: 0.8193 (tpp) REVERT: A 478 TYR cc_start: 0.8179 (t80) cc_final: 0.7836 (t80) outliers start: 20 outliers final: 18 residues processed: 115 average time/residue: 0.1360 time to fit residues: 19.8844 Evaluate side-chains 118 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7603 moved from start: 0.3128 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= 0.195 Angle : 0.660 15.897 5457 Z= 0.327 Chirality : 0.043 0.181 597 Planarity : 0.004 0.039 672 Dihedral : 4.670 24.114 511 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.20 % Allowed : 25.30 % Favored : 69.50 % 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: 1.53 (0.39), residues: 474 helix: 1.95 (0.32), residues: 231 sheet: 0.44 (0.56), residues: 75 loop : 0.07 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.029 0.002 PHE A 490 TYR 0.010 0.001 TYR A 140 ARG 0.003 0.000 ARG A 54 ********************** 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 128 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8345 (mm) cc_final: 0.8101 (mm) REVERT: A 101 MET cc_start: 0.8087 (ptp) cc_final: 0.7613 (pmm) REVERT: A 104 SER cc_start: 0.8852 (p) cc_final: 0.8513 (p) REVERT: A 219 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (pt) REVERT: A 478 TYR cc_start: 0.8166 (t80) cc_final: 0.7790 (t80) outliers start: 22 outliers final: 19 residues processed: 120 average time/residue: 0.1296 time to fit residues: 19.9920 Evaluate side-chains 126 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127616 restraints weight = 8604.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130824 restraints weight = 5096.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133085 restraints weight = 3651.364| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3262 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= 0.214 Angle : 0.663 16.062 5457 Z= 0.329 Chirality : 0.042 0.150 597 Planarity : 0.004 0.042 672 Dihedral : 4.692 24.977 511 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.96 % Allowed : 25.53 % Favored : 69.50 % 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: 1.58 (0.39), residues: 474 helix: 1.99 (0.33), residues: 231 sheet: 0.51 (0.55), residues: 75 loop : 0.07 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.002 0.001 HIS A 496 PHE 0.022 0.002 PHE A 365 TYR 0.019 0.002 TYR A 140 ARG 0.003 0.000 ARG A 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.58 seconds wall clock time: 22 minutes 59.47 seconds (1379.47 seconds total)