Starting phenix.real_space_refine on Fri Aug 2 14:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/08_2024/8qd0_18339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/08_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_18339/08_2024/8qd0_18339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/08_2024/8qd0_18339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/08_2024/8qd0_18339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qd0_18339/08_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-5409/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: 2.58, per 1000 atoms: 0.78 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: 1.39 Conformation dependent library (CDL) restraints added in 623.1 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: 0.37 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: 0.93 Time building geometry restraints manager: 1.52 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 3.120 nonbonded pdb=" OE1 GLU A 342 " pdb=" ND2 ASN A 345 " model vdw 2.371 3.120 nonbonded pdb=" O VAL A 391 " pdb=" OG1 THR A 395 " model vdw 2.444 3.040 nonbonded pdb=" NH2 ARG A 151 " pdb=" O ILE A 269 " model vdw 2.459 3.120 nonbonded pdb=" O ILE A 452 " pdb=" OG SER A 456 " model vdw 2.483 3.040 ... (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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.7575 time to fit residues: 56.2864 Evaluate side-chains 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 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: 0.7907 moved from start: 0.2202 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= 0.223 Angle : 0.639 6.852 4590 Z= 0.332 Chirality : 0.042 0.242 543 Planarity : 0.005 0.062 555 Dihedral : 4.976 55.638 454 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.25 % Allowed : 15.30 % Favored : 80.45 % 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: 1.68 (0.40), residues: 418 helix: 1.57 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.22 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.014 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.003 0.001 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: 15 poor density : 61 time to evaluate : 0.390 Fit side-chains REVERT: A 305 PHE cc_start: 0.6905 (m-80) cc_final: 0.6316 (m-80) outliers start: 15 outliers final: 1 residues processed: 69 average time/residue: 0.7423 time to fit residues: 53.6050 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE 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: 0.6980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3371 Z= 0.203 Angle : 0.600 7.527 4590 Z= 0.312 Chirality : 0.040 0.238 543 Planarity : 0.005 0.043 555 Dihedral : 4.898 54.047 454 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.12 % Allowed : 17.00 % 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: 1.91 (0.41), residues: 418 helix: 1.72 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.13 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 143 HIS 0.002 0.001 HIS A 338 PHE 0.017 0.002 PHE A 91 TYR 0.020 0.001 TYR A 94 ARG 0.001 0.000 ARG A 492 *********************** 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 71 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.375 Fit side-chains REVERT: A 305 PHE cc_start: 0.7087 (m-80) cc_final: 0.6596 (m-80) REVERT: A 429 LEU cc_start: 0.6696 (mt) cc_final: 0.6409 (mt) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 0.7457 time to fit residues: 50.8076 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 402 TRP 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3371 Z= 0.207 Angle : 0.587 6.953 4590 Z= 0.303 Chirality : 0.040 0.220 543 Planarity : 0.005 0.048 555 Dihedral : 4.846 54.037 454 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 17.85 % Favored : 78.75 % 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: 2.05 (0.41), residues: 418 helix: 1.79 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.02 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.019 0.002 PHE A 100 TYR 0.022 0.001 TYR A 94 ARG 0.002 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 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.373 Fit side-chains REVERT: A 297 TYR cc_start: 0.6994 (m-80) cc_final: 0.6511 (t80) REVERT: A 305 PHE cc_start: 0.7093 (m-80) cc_final: 0.6638 (m-80) REVERT: A 429 LEU cc_start: 0.6727 (mt) cc_final: 0.6523 (mt) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 0.7467 time to fit residues: 50.0721 Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3371 Z= 0.259 Angle : 0.609 7.832 4590 Z= 0.317 Chirality : 0.043 0.236 543 Planarity : 0.005 0.039 555 Dihedral : 4.859 50.405 454 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.40 % Allowed : 18.70 % Favored : 77.90 % 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: 1.88 (0.40), residues: 418 helix: 1.64 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.87 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.003 0.001 HIS A 338 PHE 0.015 0.002 PHE A 91 TYR 0.023 0.001 TYR A 94 ARG 0.001 0.000 ARG A 492 *********************** 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 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.366 Fit side-chains REVERT: A 274 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6742 (tt0) REVERT: A 297 TYR cc_start: 0.7064 (m-80) cc_final: 0.6511 (t80) REVERT: A 437 ILE cc_start: 0.7646 (mm) cc_final: 0.7237 (mm) outliers start: 12 outliers final: 4 residues processed: 63 average time/residue: 0.7459 time to fit residues: 49.2446 Evaluate side-chains 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 402 TRP 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: 0.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.3283 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= 0.207 Angle : 0.580 6.828 4590 Z= 0.304 Chirality : 0.041 0.238 543 Planarity : 0.005 0.050 555 Dihedral : 4.930 53.879 454 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.12 % Allowed : 21.25 % Favored : 75.64 % 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: 2.02 (0.40), residues: 418 helix: 1.73 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.77 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 102 HIS 0.002 0.001 HIS A 338 PHE 0.023 0.002 PHE A 100 TYR 0.022 0.001 TYR A 94 ARG 0.001 0.000 ARG A 370 *********************** 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: 11 poor density : 61 time to evaluate : 0.371 Fit side-chains REVERT: A 297 TYR cc_start: 0.7057 (m-80) cc_final: 0.6496 (t80) REVERT: A 429 LEU cc_start: 0.6765 (mt) cc_final: 0.6488 (mt) REVERT: A 437 ILE cc_start: 0.7569 (mm) cc_final: 0.7184 (mm) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.7492 time to fit residues: 54.0562 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 444 ILE 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: 1.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 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: 0.7910 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3371 Z= 0.195 Angle : 0.590 7.496 4590 Z= 0.308 Chirality : 0.041 0.234 543 Planarity : 0.005 0.037 555 Dihedral : 4.956 54.929 454 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.55 % Allowed : 22.95 % 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: 2.14 (0.41), residues: 418 helix: 1.80 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.65 (0.74), residues: 64 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 0.016 0.001 PHE A 100 TYR 0.022 0.001 TYR A 392 ARG 0.007 0.000 ARG A 82 *********************** 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 66 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.421 Fit side-chains REVERT: A 297 TYR cc_start: 0.7097 (m-80) cc_final: 0.6589 (t80) REVERT: A 411 MET cc_start: 0.8635 (ttm) cc_final: 0.8407 (ttp) REVERT: A 429 LEU cc_start: 0.6639 (mt) cc_final: 0.6396 (mt) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.6882 time to fit residues: 45.6419 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 444 ILE 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: 1.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3573 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= 0.197 Angle : 0.593 7.913 4590 Z= 0.311 Chirality : 0.041 0.237 543 Planarity : 0.005 0.047 555 Dihedral : 4.980 54.564 454 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.83 % Allowed : 22.38 % 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: 2.32 (0.41), residues: 418 helix: 1.90 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.37 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 102 HIS 0.004 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.006 0.000 ARG A 82 *********************** 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 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.371 Fit side-chains REVERT: A 297 TYR cc_start: 0.7103 (m-80) cc_final: 0.6595 (t80) REVERT: A 429 LEU cc_start: 0.6472 (mt) cc_final: 0.6236 (mt) REVERT: A 483 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8279 (tt) outliers start: 10 outliers final: 3 residues processed: 62 average time/residue: 0.7126 time to fit residues: 46.4544 Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3651 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 : 0.608 8.076 4590 Z= 0.317 Chirality : 0.041 0.234 543 Planarity : 0.005 0.037 555 Dihedral : 4.941 53.170 454 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.42 % Allowed : 24.36 % 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: 1.92 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.32 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 102 HIS 0.008 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.027 0.001 TYR A 392 ARG 0.006 0.000 ARG A 82 *********************** 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 60 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.391 Fit side-chains REVERT: A 297 TYR cc_start: 0.7100 (m-80) cc_final: 0.6594 (t80) REVERT: A 389 MET cc_start: 0.8221 (tpt) cc_final: 0.7820 (tpt) REVERT: A 429 LEU cc_start: 0.6431 (mt) cc_final: 0.6180 (mt) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 0.7090 time to fit residues: 44.0064 Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3371 Z= 0.240 Angle : 0.646 8.573 4590 Z= 0.336 Chirality : 0.042 0.236 543 Planarity : 0.005 0.048 555 Dihedral : 4.935 51.140 454 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.42 % Allowed : 24.65 % Favored : 73.94 % 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: 2.29 (0.40), residues: 418 helix: 1.88 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.41 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 102 HIS 0.009 0.001 HIS A 338 PHE 0.015 0.002 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.006 0.000 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 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.384 Fit side-chains REVERT: A 253 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.8018 (ttp) REVERT: A 297 TYR cc_start: 0.7172 (m-80) cc_final: 0.6688 (t80) REVERT: A 429 LEU cc_start: 0.6438 (mt) cc_final: 0.6203 (mt) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.7630 time to fit residues: 45.6199 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134027 restraints weight = 4237.028| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.31 r_work: 0.3492 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3371 Z= 0.217 Angle : 0.637 8.545 4590 Z= 0.331 Chirality : 0.041 0.233 543 Planarity : 0.005 0.041 555 Dihedral : 4.957 52.430 454 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.13 % Allowed : 25.21 % Favored : 73.65 % 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: 2.37 (0.40), residues: 418 helix: 1.92 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.27 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 102 HIS 0.007 0.001 HIS A 338 PHE 0.014 0.001 PHE A 472 TYR 0.022 0.001 TYR A 94 ARG 0.006 0.000 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.64 seconds wall clock time: 26 minutes 31.84 seconds (1591.84 seconds total)