Starting phenix.real_space_refine on Tue Feb 13 18:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/02_2024/6coy_7544.pdb" } resolution = 3.36 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= 0.003 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 4 4.86 5 C 4776 2.51 5 N 1130 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.31, per 1000 atoms: 0.60 Number of scatterers: 7156 At special positions: 0 Unit cell: (110.21, 77.25, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 58 16.00 O 1188 8.00 N 1130 7.00 C 4776 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 78.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 156 through 183 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 299 through 323 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 379 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 117 through 152 Processing helix chain 'B' and resid 156 through 183 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 299 through 323 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 512 551 hydrogen bonds defined for protein. 1551 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: 2.24 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1096 1.31 - 1.43: 2014 1.43 - 1.56: 4140 1.56 - 1.68: 4 1.68 - 1.81: 98 Bond restraints: 7352 Sorted by residual: bond pdb=" CB ILE A 556 " pdb=" CG1 ILE A 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB ILE B 556 " pdb=" CG1 ILE B 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB HIS B 538 " pdb=" CG HIS B 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB HIS A 538 " pdb=" CG HIS A 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB ILE B 553 " pdb=" CG1 ILE B 553 " ideal model delta sigma weight residual 1.530 1.431 0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.24: 220 105.24 - 112.41: 3618 112.41 - 119.58: 2560 119.58 - 126.76: 3528 126.76 - 133.93: 80 Bond angle restraints: 10006 Sorted by residual: angle pdb=" C THR B 281 " pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C THR A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C LEU A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C LEU B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C PHE B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 119.56 125.93 -6.37 1.01e+00 9.80e-01 3.97e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4126 17.23 - 34.46: 86 34.46 - 51.69: 18 51.69 - 68.91: 18 68.91 - 86.14: 6 Dihedral angle restraints: 4254 sinusoidal: 1592 harmonic: 2662 Sorted by residual: dihedral pdb=" CA THR B 432 " pdb=" C THR B 432 " pdb=" N TRP B 433 " pdb=" CA TRP B 433 " ideal model delta harmonic sigma weight residual 180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA THR A 432 " pdb=" C THR A 432 " pdb=" N TRP A 433 " pdb=" CA TRP A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C TYR B 393 " pdb=" N TYR B 393 " pdb=" CA TYR B 393 " pdb=" CB TYR B 393 " ideal model delta harmonic sigma weight residual -122.60 -130.59 7.99 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 684 0.069 - 0.139: 342 0.139 - 0.208: 102 0.208 - 0.278: 34 0.278 - 0.347: 8 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 407 " pdb=" N PRO B 407 " pdb=" C PRO B 407 " pdb=" CB PRO B 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 558 " pdb=" N PRO B 558 " pdb=" C PRO B 558 " pdb=" CB PRO B 558 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1167 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 590 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 591 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 590 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO A 591 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 485 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 486 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " 0.056 5.00e-02 4.00e+02 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1662 2.77 - 3.31: 7383 3.31 - 3.84: 12334 3.84 - 4.37: 14469 4.37 - 4.90: 24411 Nonbonded interactions: 60259 Sorted by model distance: nonbonded pdb=" N GLN A 185 " pdb=" OE1 GLN A 185 " model vdw 2.242 2.520 nonbonded pdb=" N GLN B 185 " pdb=" OE1 GLN B 185 " model vdw 2.242 2.520 nonbonded pdb=" CB GLU A 291 " pdb=" OE1 GLU A 291 " model vdw 2.449 2.752 nonbonded pdb=" CB GLU B 291 " pdb=" OE1 GLU B 291 " model vdw 2.449 2.752 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 539 " model vdw 2.501 2.440 ... (remaining 60254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 7.420 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.020 0.153 7352 Z= 1.323 Angle : 1.425 13.192 10006 Z= 0.978 Chirality : 0.091 0.347 1170 Planarity : 0.014 0.150 1224 Dihedral : 10.542 86.142 2546 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.82 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 922 helix: 0.29 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 322 HIS 0.007 0.002 HIS B 436 PHE 0.029 0.005 PHE A 547 TYR 0.044 0.010 TYR B 296 ARG 0.006 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1427 time to fit residues: 25.7272 Evaluate side-chains 82 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 436 HIS A 538 HIS B 160 GLN B 436 HIS B 538 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7352 Z= 0.254 Angle : 0.605 6.579 10006 Z= 0.326 Chirality : 0.043 0.154 1170 Planarity : 0.007 0.070 1224 Dihedral : 4.163 14.702 978 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.31 % Allowed : 6.56 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.28), residues: 922 helix: 1.94 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -0.74 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.004 0.001 HIS A 451 PHE 0.030 0.002 PHE A 547 TYR 0.009 0.001 TYR A 137 ARG 0.002 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.832 Fit side-chains REVERT: A 325 ASP cc_start: 0.8141 (t0) cc_final: 0.7625 (t0) REVERT: A 346 LYS cc_start: 0.8157 (mttt) cc_final: 0.7927 (mptt) REVERT: B 325 ASP cc_start: 0.8135 (t0) cc_final: 0.7624 (t0) REVERT: B 346 LYS cc_start: 0.8156 (mttt) cc_final: 0.7926 (mptt) outliers start: 10 outliers final: 4 residues processed: 134 average time/residue: 0.1481 time to fit residues: 28.6847 Evaluate side-chains 112 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.0020 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.0370 chunk 67 optimal weight: 0.9990 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS B 369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7352 Z= 0.192 Angle : 0.518 5.860 10006 Z= 0.276 Chirality : 0.041 0.141 1170 Planarity : 0.006 0.060 1224 Dihedral : 3.781 13.179 978 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.84 % Allowed : 8.40 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.28), residues: 922 helix: 2.70 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS B 379 PHE 0.030 0.001 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.879 Fit side-chains REVERT: A 325 ASP cc_start: 0.8338 (t0) cc_final: 0.7888 (t0) REVERT: A 346 LYS cc_start: 0.7958 (mttt) cc_final: 0.7729 (mptt) REVERT: B 325 ASP cc_start: 0.8338 (t0) cc_final: 0.7886 (t0) REVERT: B 346 LYS cc_start: 0.7963 (mttt) cc_final: 0.7734 (mptt) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.1542 time to fit residues: 24.2163 Evaluate side-chains 104 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 0.0270 chunk 43 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7352 Z= 0.192 Angle : 0.506 5.861 10006 Z= 0.263 Chirality : 0.041 0.137 1170 Planarity : 0.006 0.058 1224 Dihedral : 3.707 13.682 978 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.57 % Allowed : 10.24 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.28), residues: 922 helix: 2.84 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.44 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE B 547 TYR 0.008 0.001 TYR A 146 ARG 0.001 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.875 Fit side-chains REVERT: A 204 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7542 (ptmm) REVERT: A 325 ASP cc_start: 0.8359 (t0) cc_final: 0.7879 (t0) REVERT: B 204 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7542 (ptmm) REVERT: B 325 ASP cc_start: 0.8359 (t0) cc_final: 0.7875 (t0) outliers start: 12 outliers final: 12 residues processed: 110 average time/residue: 0.1531 time to fit residues: 24.6498 Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7352 Z= 0.234 Angle : 0.515 5.733 10006 Z= 0.270 Chirality : 0.041 0.136 1170 Planarity : 0.006 0.055 1224 Dihedral : 3.635 14.425 978 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 9.71 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.28), residues: 922 helix: 2.83 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.003 0.001 HIS A 451 PHE 0.028 0.002 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.787 Fit side-chains REVERT: A 204 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7599 (ptmm) REVERT: A 325 ASP cc_start: 0.8420 (t0) cc_final: 0.7932 (t0) REVERT: B 204 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7598 (ptmm) REVERT: B 325 ASP cc_start: 0.8420 (t0) cc_final: 0.7930 (t0) outliers start: 22 outliers final: 12 residues processed: 122 average time/residue: 0.1641 time to fit residues: 28.1849 Evaluate side-chains 124 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8199 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7352 Z= 0.210 Angle : 0.506 5.893 10006 Z= 0.264 Chirality : 0.041 0.134 1170 Planarity : 0.005 0.054 1224 Dihedral : 3.618 14.845 978 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 9.84 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.28), residues: 922 helix: 2.93 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS B 451 PHE 0.028 0.001 PHE A 547 TYR 0.008 0.001 TYR A 137 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.716 Fit side-chains REVERT: A 235 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 325 ASP cc_start: 0.8398 (t0) cc_final: 0.7888 (t0) REVERT: B 235 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7647 (t80) REVERT: B 325 ASP cc_start: 0.8397 (t0) cc_final: 0.7883 (t0) outliers start: 20 outliers final: 18 residues processed: 124 average time/residue: 0.1384 time to fit residues: 25.8438 Evaluate side-chains 124 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7352 Z= 0.251 Angle : 0.531 5.781 10006 Z= 0.276 Chirality : 0.042 0.139 1170 Planarity : 0.005 0.053 1224 Dihedral : 3.626 14.689 978 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 10.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.28), residues: 922 helix: 2.81 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS B 369 PHE 0.029 0.002 PHE A 547 TYR 0.008 0.001 TYR A 137 ARG 0.002 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.823 Fit side-chains REVERT: A 235 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 325 ASP cc_start: 0.8453 (t0) cc_final: 0.7933 (t0) REVERT: B 235 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7680 (t80) REVERT: B 325 ASP cc_start: 0.8458 (t0) cc_final: 0.7934 (t0) outliers start: 22 outliers final: 20 residues processed: 116 average time/residue: 0.1480 time to fit residues: 25.9201 Evaluate side-chains 120 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7352 Z= 0.215 Angle : 0.513 6.446 10006 Z= 0.267 Chirality : 0.041 0.135 1170 Planarity : 0.005 0.052 1224 Dihedral : 3.611 15.014 978 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 10.24 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.28), residues: 922 helix: 2.88 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE A 547 TYR 0.008 0.001 TYR A 137 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.916 Fit side-chains REVERT: A 235 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7726 (t80) REVERT: A 325 ASP cc_start: 0.8448 (t0) cc_final: 0.7916 (t0) REVERT: B 235 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 325 ASP cc_start: 0.8446 (t0) cc_final: 0.7915 (t0) outliers start: 22 outliers final: 20 residues processed: 116 average time/residue: 0.1484 time to fit residues: 25.8022 Evaluate side-chains 126 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7352 Z= 0.198 Angle : 0.513 7.169 10006 Z= 0.265 Chirality : 0.040 0.134 1170 Planarity : 0.005 0.052 1224 Dihedral : 3.554 15.051 978 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 10.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.28), residues: 922 helix: 2.89 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.027 0.001 PHE B 547 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.799 Fit side-chains REVERT: A 235 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 325 ASP cc_start: 0.8448 (t0) cc_final: 0.7908 (t0) REVERT: B 235 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 325 ASP cc_start: 0.8446 (t0) cc_final: 0.7909 (t0) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.1366 time to fit residues: 23.5431 Evaluate side-chains 120 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7352 Z= 0.191 Angle : 0.515 7.822 10006 Z= 0.265 Chirality : 0.041 0.134 1170 Planarity : 0.005 0.051 1224 Dihedral : 3.515 15.096 978 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 11.29 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.28), residues: 922 helix: 2.94 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.43 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.027 0.001 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.001 0.000 ARG B 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.813 Fit side-chains REVERT: A 235 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 325 ASP cc_start: 0.8409 (t0) cc_final: 0.7857 (t0) REVERT: B 235 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 325 ASP cc_start: 0.8407 (t0) cc_final: 0.7858 (t0) outliers start: 22 outliers final: 20 residues processed: 114 average time/residue: 0.1365 time to fit residues: 23.3854 Evaluate side-chains 128 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.0050 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.121803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104589 restraints weight = 8565.760| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.83 r_work: 0.2961 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7352 Z= 0.177 Angle : 0.506 7.585 10006 Z= 0.261 Chirality : 0.040 0.134 1170 Planarity : 0.005 0.051 1224 Dihedral : 3.464 15.281 978 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.89 % Allowed : 10.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.28), residues: 922 helix: 2.99 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS B 451 PHE 0.026 0.001 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.001 0.000 ARG B 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.65 seconds wall clock time: 31 minutes 56.89 seconds (1916.89 seconds total)