Starting phenix.real_space_refine on Thu Jul 18 19:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/07_2024/8qd0_18339.cif" } resolution = 2.8 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= 0.098 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 19 5.16 5 C 2187 2.51 5 N 522 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3290 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3283 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.76 Number of scatterers: 3290 At special positions: 0 Unit cell: (83.658, 56.154, 65.322, 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 19 16.00 O 562 8.00 N 522 7.00 C 2187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.43 Conformation dependent library (CDL) restraints added in 559.8 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 82 through 107 removed outlier: 4.255A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.096A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 168 removed outlier: 3.922A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 5.138A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 7.574A pdb=" N LEU A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ARG A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.646A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.557A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 242 through 272 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.789A pdb=" N PHE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.552A pdb=" N ALA A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.526A pdb=" N MET A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 372 Processing helix chain 'A' and resid 373 through 396 Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.653A pdb=" N PHE A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) Proline residue: A 420 - end of helix removed outlier: 3.815A pdb=" N PHE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 465 removed outlier: 3.609A pdb=" N SER A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 486 removed outlier: 3.694A pdb=" N GLY A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 271 hydrogen bonds defined for protein. 810 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: 0.85 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 608 1.33 - 1.45: 840 1.45 - 1.57: 1892 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3371 Sorted by residual: bond pdb=" N LEU A 441 " pdb=" CA LEU A 441 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N PRO A 276 " pdb=" CA PRO A 276 " ideal model delta sigma weight residual 1.467 1.434 0.033 1.24e-02 6.50e+03 7.16e+00 bond pdb=" N GLU A 435 " pdb=" CA GLU A 435 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.25e-02 6.40e+03 4.92e+00 bond pdb=" C LEU A 441 " pdb=" O LEU A 441 " ideal model delta sigma weight residual 1.237 1.215 0.021 1.19e-02 7.06e+03 3.25e+00 bond pdb=" C PRO A 276 " pdb=" O PRO A 276 " ideal model delta sigma weight residual 1.233 1.211 0.022 1.24e-02 6.50e+03 3.08e+00 ... (remaining 3366 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.73: 58 104.73 - 112.06: 1726 112.06 - 119.39: 1041 119.39 - 126.73: 1713 126.73 - 134.06: 52 Bond angle restraints: 4590 Sorted by residual: angle pdb=" CA PRO A 198 " pdb=" N PRO A 198 " pdb=" CD PRO A 198 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" C PRO A 276 " pdb=" CA PRO A 276 " pdb=" CB PRO A 276 " ideal model delta sigma weight residual 111.40 106.40 5.00 1.54e+00 4.22e-01 1.05e+01 angle pdb=" N VAL A 237 " pdb=" CA VAL A 237 " pdb=" C VAL A 237 " ideal model delta sigma weight residual 108.15 111.20 -3.05 9.90e-01 1.02e+00 9.47e+00 angle pdb=" N PRO A 198 " pdb=" CD PRO A 198 " pdb=" CG PRO A 198 " ideal model delta sigma weight residual 103.20 98.66 4.54 1.50e+00 4.44e-01 9.16e+00 angle pdb=" N LEU A 441 " pdb=" CA LEU A 441 " pdb=" C LEU A 441 " ideal model delta sigma weight residual 111.36 108.09 3.27 1.09e+00 8.42e-01 9.00e+00 ... (remaining 4585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1725 17.49 - 34.99: 159 34.99 - 52.48: 45 52.48 - 69.97: 5 69.97 - 87.47: 5 Dihedral angle restraints: 1939 sinusoidal: 728 harmonic: 1211 Sorted by residual: dihedral pdb=" CA MET A 197 " pdb=" C MET A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CD ARG A 333 " pdb=" NE ARG A 333 " pdb=" CZ ARG A 333 " pdb=" NH1 ARG A 333 " ideal model delta sinusoidal sigma weight residual 0.00 -30.26 30.26 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA ASN A 320 " pdb=" CB ASN A 320 " pdb=" CG ASN A 320 " pdb=" OD1 ASN A 320 " ideal model delta sinusoidal sigma weight residual 120.00 -166.69 -73.31 2 2.00e+01 2.50e-03 1.10e+01 ... (remaining 1936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 427 0.046 - 0.092: 101 0.092 - 0.138: 14 0.138 - 0.184: 0 0.184 - 0.230: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA PRO A 432 " pdb=" N PRO A 432 " pdb=" C PRO A 432 " pdb=" CB PRO A 432 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 540 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " 0.563 9.50e-02 1.11e+02 2.52e-01 3.89e+01 pdb=" NE ARG A 333 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 197 " 0.065 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO A 198 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.009 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP A 143 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.000 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1160 2.85 - 3.36: 3528 3.36 - 3.87: 5734 3.87 - 4.39: 6688 4.39 - 4.90: 11284 Nonbonded interactions: 28394 Sorted by model distance: nonbonded pdb=" OE1 GLN A 101 " pdb=" NZ LYS A 168 " model vdw 2.337 2.520 nonbonded pdb=" OE1 GLU A 342 " pdb=" ND2 ASN A 345 " model vdw 2.371 2.520 nonbonded pdb=" O VAL A 391 " pdb=" OG1 THR A 395 " model vdw 2.444 2.440 nonbonded pdb=" NH2 ARG A 151 " pdb=" O ILE A 269 " model vdw 2.459 2.520 nonbonded pdb=" O ILE A 452 " pdb=" OG SER A 456 " model vdw 2.483 2.440 ... (remaining 28389 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3371 Z= 0.197 Angle : 0.634 8.706 4590 Z= 0.358 Chirality : 0.038 0.230 543 Planarity : 0.012 0.252 555 Dihedral : 15.295 87.467 1167 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.25 (0.41), residues: 418 helix: 1.22 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.70 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.009 0.001 PHE A 310 TYR 0.015 0.001 TYR A 94 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.357 Fit side-chains REVERT: A 131 MET cc_start: 0.9037 (mtp) cc_final: 0.8684 (mtp) REVERT: A 143 TRP cc_start: 0.7567 (t60) cc_final: 0.7112 (t60) REVERT: A 297 TYR cc_start: 0.7128 (m-80) cc_final: 0.6641 (t80) REVERT: A 305 PHE cc_start: 0.7155 (m-80) cc_final: 0.6620 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.7501 time to fit residues: 55.6633 Evaluate side-chains 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 223 GLN A 307 ASN A 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3371 Z= 0.217 Angle : 0.623 6.729 4590 Z= 0.324 Chirality : 0.041 0.236 543 Planarity : 0.005 0.059 555 Dihedral : 4.944 55.255 454 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.68 % Allowed : 16.43 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.82 (0.40), residues: 418 helix: 1.67 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.26 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 143 HIS 0.002 0.001 HIS A 249 PHE 0.015 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.362 Fit side-chains REVERT: A 109 ASN cc_start: 0.8139 (t0) cc_final: 0.7927 (t160) REVERT: A 113 MET cc_start: 0.7320 (mtm) cc_final: 0.6952 (mtm) REVERT: A 305 PHE cc_start: 0.6924 (m-80) cc_final: 0.6492 (m-80) outliers start: 13 outliers final: 3 residues processed: 69 average time/residue: 0.7135 time to fit residues: 51.5218 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3371 Z= 0.181 Angle : 0.586 7.639 4590 Z= 0.301 Chirality : 0.040 0.230 543 Planarity : 0.005 0.038 555 Dihedral : 4.894 56.062 454 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.25 % Allowed : 16.43 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.23 (0.41), residues: 418 helix: 1.90 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.94 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.002 0.000 HIS A 338 PHE 0.015 0.002 PHE A 91 TYR 0.021 0.001 TYR A 94 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.366 Fit side-chains REVERT: A 109 ASN cc_start: 0.8183 (t0) cc_final: 0.7909 (t160) REVERT: A 113 MET cc_start: 0.7395 (mtm) cc_final: 0.7050 (mtm) REVERT: A 297 TYR cc_start: 0.7007 (m-80) cc_final: 0.6511 (t80) REVERT: A 305 PHE cc_start: 0.7088 (m-80) cc_final: 0.6626 (m-80) REVERT: A 402 TRP cc_start: 0.6268 (OUTLIER) cc_final: 0.5821 (p-90) outliers start: 15 outliers final: 4 residues processed: 70 average time/residue: 0.7065 time to fit residues: 51.7645 Evaluate side-chains 52 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 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: 0.7913 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3371 Z= 0.201 Angle : 0.584 7.033 4590 Z= 0.301 Chirality : 0.041 0.226 543 Planarity : 0.005 0.044 555 Dihedral : 4.815 53.578 454 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.82 % Allowed : 16.71 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.31 (0.41), residues: 418 helix: 1.95 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.83 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.017 0.002 PHE A 100 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.368 Fit side-chains REVERT: A 109 ASN cc_start: 0.8084 (t0) cc_final: 0.7874 (t0) REVERT: A 113 MET cc_start: 0.7458 (mtm) cc_final: 0.7256 (ttm) REVERT: A 127 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 297 TYR cc_start: 0.6998 (m-80) cc_final: 0.6444 (t80) REVERT: A 305 PHE cc_start: 0.7136 (m-80) cc_final: 0.6688 (m-80) REVERT: A 429 LEU cc_start: 0.6706 (mt) cc_final: 0.6442 (mt) REVERT: A 437 ILE cc_start: 0.7621 (mm) cc_final: 0.7203 (mm) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 0.6392 time to fit residues: 49.0112 Evaluate side-chains 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3371 Z= 0.371 Angle : 0.664 8.034 4590 Z= 0.345 Chirality : 0.045 0.234 543 Planarity : 0.005 0.045 555 Dihedral : 4.901 46.591 454 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.53 % Allowed : 17.85 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.89 (0.40), residues: 418 helix: 1.60 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.43 (0.74), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 402 HIS 0.003 0.001 HIS A 338 PHE 0.023 0.002 PHE A 206 TYR 0.028 0.002 TYR A 94 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.379 Fit side-chains REVERT: A 113 MET cc_start: 0.7495 (mtm) cc_final: 0.7249 (ttm) REVERT: A 242 ASP cc_start: 0.7808 (t0) cc_final: 0.7483 (t0) REVERT: A 274 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: A 297 TYR cc_start: 0.7126 (m-80) cc_final: 0.6517 (t80) REVERT: A 370 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.5800 (mtt90) REVERT: A 437 ILE cc_start: 0.7707 (mm) cc_final: 0.7341 (mm) outliers start: 16 outliers final: 8 residues processed: 67 average time/residue: 0.7132 time to fit residues: 50.0965 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3371 Z= 0.205 Angle : 0.586 7.081 4590 Z= 0.304 Chirality : 0.040 0.230 543 Planarity : 0.005 0.052 555 Dihedral : 4.946 54.010 454 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.68 % Allowed : 19.83 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.24 (0.40), residues: 418 helix: 1.89 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.78 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.022 0.002 PHE A 100 TYR 0.021 0.001 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.358 Fit side-chains REVERT: A 109 ASN cc_start: 0.7897 (t0) cc_final: 0.7475 (t0) REVERT: A 113 MET cc_start: 0.7415 (mtm) cc_final: 0.7167 (mtm) REVERT: A 127 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8496 (m) REVERT: A 297 TYR cc_start: 0.7141 (m-80) cc_final: 0.6583 (t80) REVERT: A 370 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5768 (mpt180) REVERT: A 437 ILE cc_start: 0.7596 (mm) cc_final: 0.7233 (mm) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 0.7599 time to fit residues: 52.4539 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3371 Z= 0.291 Angle : 0.636 8.080 4590 Z= 0.329 Chirality : 0.043 0.228 543 Planarity : 0.005 0.039 555 Dihedral : 4.883 48.621 454 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.97 % Allowed : 20.68 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.06 (0.40), residues: 418 helix: 1.77 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.82 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.028 0.002 PHE A 100 TYR 0.024 0.002 TYR A 94 ARG 0.001 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.368 Fit side-chains REVERT: A 109 ASN cc_start: 0.8012 (t0) cc_final: 0.7557 (t0) REVERT: A 113 MET cc_start: 0.7435 (mtm) cc_final: 0.7071 (mtm) REVERT: A 127 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 272 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: A 297 TYR cc_start: 0.7159 (m-80) cc_final: 0.6559 (t80) REVERT: A 437 ILE cc_start: 0.7657 (mm) cc_final: 0.7284 (mm) outliers start: 14 outliers final: 6 residues processed: 65 average time/residue: 0.6480 time to fit residues: 44.1784 Evaluate side-chains 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3371 Z= 0.184 Angle : 0.600 8.124 4590 Z= 0.310 Chirality : 0.040 0.225 543 Planarity : 0.005 0.055 555 Dihedral : 4.958 55.369 454 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.25 % Allowed : 20.96 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.44 (0.41), residues: 418 helix: 2.01 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.60 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.019 0.002 PHE A 100 TYR 0.020 0.001 TYR A 94 ARG 0.001 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.400 Fit side-chains REVERT: A 109 ASN cc_start: 0.7782 (t0) cc_final: 0.7566 (t0) REVERT: A 113 MET cc_start: 0.7317 (mtm) cc_final: 0.6989 (mtm) REVERT: A 127 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 297 TYR cc_start: 0.7024 (m-80) cc_final: 0.6502 (t80) REVERT: A 370 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5995 (mpt180) REVERT: A 402 TRP cc_start: 0.6099 (OUTLIER) cc_final: 0.5696 (p-90) REVERT: A 437 ILE cc_start: 0.7631 (mm) cc_final: 0.7288 (mm) outliers start: 15 outliers final: 4 residues processed: 66 average time/residue: 0.6723 time to fit residues: 46.7791 Evaluate side-chains 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3371 Z= 0.216 Angle : 0.624 8.384 4590 Z= 0.318 Chirality : 0.041 0.226 543 Planarity : 0.005 0.039 555 Dihedral : 4.862 51.546 454 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.12 % Allowed : 22.66 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.36 (0.40), residues: 418 helix: 1.97 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.68 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 102 HIS 0.006 0.001 HIS A 338 PHE 0.017 0.002 PHE A 100 TYR 0.026 0.001 TYR A 392 ARG 0.001 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.315 Fit side-chains REVERT: A 109 ASN cc_start: 0.7831 (t0) cc_final: 0.7598 (t0) REVERT: A 113 MET cc_start: 0.7357 (mtm) cc_final: 0.7014 (mtm) REVERT: A 127 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8483 (m) REVERT: A 297 TYR cc_start: 0.7047 (m-80) cc_final: 0.6602 (t80) REVERT: A 370 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.5976 (mpt180) REVERT: A 495 LYS cc_start: 0.8030 (tptt) cc_final: 0.7709 (tptp) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.7445 time to fit residues: 49.1268 Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3371 Z= 0.195 Angle : 0.623 8.805 4590 Z= 0.317 Chirality : 0.041 0.223 543 Planarity : 0.005 0.055 555 Dihedral : 4.911 53.815 454 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 22.10 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.59 (0.40), residues: 418 helix: 2.10 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.48 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 102 HIS 0.004 0.001 HIS A 338 PHE 0.015 0.002 PHE A 100 TYR 0.022 0.001 TYR A 94 ARG 0.007 0.001 ARG A 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.375 Fit side-chains REVERT: A 109 ASN cc_start: 0.7843 (t0) cc_final: 0.7607 (t0) REVERT: A 113 MET cc_start: 0.7312 (mtm) cc_final: 0.6974 (mtm) REVERT: A 127 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8461 (m) REVERT: A 297 TYR cc_start: 0.7017 (m-80) cc_final: 0.6630 (t80) REVERT: A 370 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6073 (mpt180) REVERT: A 402 TRP cc_start: 0.6095 (OUTLIER) cc_final: 0.5676 (p-90) outliers start: 12 outliers final: 4 residues processed: 60 average time/residue: 0.6871 time to fit residues: 43.3118 Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 456 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.159489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133123 restraints weight = 4232.187| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.27 r_work: 0.3491 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3371 Z= 0.210 Angle : 0.636 8.628 4590 Z= 0.323 Chirality : 0.041 0.223 543 Planarity : 0.005 0.041 555 Dihedral : 4.862 51.351 454 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.83 % Allowed : 22.95 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.51 (0.40), residues: 418 helix: 2.06 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.53 (0.69), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 102 HIS 0.004 0.001 HIS A 338 PHE 0.018 0.002 PHE A 100 TYR 0.023 0.001 TYR A 94 ARG 0.007 0.000 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.35 seconds wall clock time: 27 minutes 38.81 seconds (1658.81 seconds total)