Starting phenix.real_space_refine on Sun Mar 10 19:15:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/03_2024/7y7w_33672_updated.pdb" } resolution = 2.4 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= 0.002 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2844 2.51 5 N 655 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4310 Unusual residues: {' CL': 1, ' NA': 2, 'ABU': 1, 'NAG': 3} Classifications: {'peptide': 529, 'undetermined': 7, 'water': 48} Link IDs: {'PTRANS': 22, 'TRANS': 506, None: 55} Not linked: pdbres="ILE A 577 " pdbres="ABU A 701 " Not linked: pdbres="ABU A 701 " pdbres="NAG A 702 " Not linked: pdbres="NAG A 702 " pdbres="NAG A 703 " Not linked: pdbres="NAG A 703 " pdbres="NAG A 704 " Not linked: pdbres="NAG A 704 " pdbres=" NA A 705 " ... (remaining 50 not shown) Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.69 Number of scatterers: 4310 At special positions: 0 Unit cell: (67.115, 72.5275, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 774 8.00 N 655 7.00 C 2844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.08 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 792.9 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.627A pdb=" N ILE A 84 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 154 removed outlier: 4.455A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 240 through 258 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.579A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.580A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 349 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 373 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 378 through 411 removed outlier: 3.720A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 438 removed outlier: 4.701A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.760A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 531 through 558 removed outlier: 4.996A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix removed outlier: 3.550A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.460A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 620 1.29 - 1.42: 1312 1.42 - 1.55: 2407 1.55 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 4393 Sorted by residual: bond pdb=" C ASP A 395 " pdb=" O ASP A 395 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C PHE A 53 " pdb=" O PHE A 53 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.01e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.75e+00 ... (remaining 4388 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 90 105.83 - 112.88: 2238 112.88 - 119.94: 1636 119.94 - 127.00: 1946 127.00 - 134.06: 72 Bond angle restraints: 5982 Sorted by residual: angle pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.42 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 105.81 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 120.85 115.79 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.58 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 5977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2177 17.95 - 35.90: 257 35.90 - 53.86: 63 53.86 - 71.81: 15 71.81 - 89.76: 6 Dihedral angle restraints: 2518 sinusoidal: 995 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -49.63 -36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 663 0.277 - 0.554: 1 0.554 - 0.831: 0 0.831 - 1.108: 0 1.108 - 1.385: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 663 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.101 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" CG ASN A 181 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.307 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.134 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN A 184 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.203 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.064 2.00e-02 2.50e+03 6.39e-02 5.11e+01 pdb=" CG ASN A 176 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.077 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.10: 3270 3.10 - 3.70: 7039 3.70 - 4.30: 10496 4.30 - 4.90: 16729 Nonbonded interactions: 37574 Sorted by model distance: nonbonded pdb=" O HOH A 805 " pdb=" O HOH A 828 " model vdw 1.907 2.440 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 806 " model vdw 2.000 2.440 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 2.008 2.440 nonbonded pdb=" O LEU A 298 " pdb=" O HOH A 802 " model vdw 2.030 2.440 nonbonded pdb=" OG1 THR A 290 " pdb=" O HOH A 803 " model vdw 2.045 2.440 ... (remaining 37569 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: 0.340 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: 1.880 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.006 0.072 4393 Z= 0.358 Angle : 0.777 11.117 5982 Z= 0.474 Chirality : 0.084 1.385 666 Planarity : 0.005 0.042 725 Dihedral : 17.204 89.759 1549 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 26.73 % Favored : 72.16 % 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: 0.06 (0.36), residues: 527 helix: 0.63 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 500 HIS 0.007 0.002 HIS A 198 PHE 0.026 0.003 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.007 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.473 Fit side-chains REVERT: A 51 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 121 MET cc_start: 0.8983 (ptm) cc_final: 0.8730 (ptp) REVERT: A 163 GLN cc_start: 0.8134 (mt0) cc_final: 0.7193 (pm20) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.2075 time to fit residues: 81.6143 Evaluate side-chains 55 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 338 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 198 HIS A 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4393 Z= 0.174 Angle : 0.572 8.416 5982 Z= 0.292 Chirality : 0.043 0.351 666 Planarity : 0.004 0.036 725 Dihedral : 6.708 59.462 643 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.45 % Allowed : 20.49 % Favored : 75.06 % 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: 0.74 (0.37), residues: 527 helix: 1.20 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 496 HIS 0.002 0.001 HIS A 347 PHE 0.029 0.002 PHE A 398 TYR 0.015 0.001 TYR A 72 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.493 Fit side-chains REVERT: A 72 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8526 (p90) REVERT: A 121 MET cc_start: 0.8927 (ptm) cc_final: 0.8726 (ptp) REVERT: A 163 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: A 481 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7654 (t80) REVERT: A 572 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5716 (mm110) outliers start: 20 outliers final: 8 residues processed: 77 average time/residue: 1.0188 time to fit residues: 82.1811 Evaluate side-chains 64 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 572 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 50.0000 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.177 Angle : 0.544 7.790 5982 Z= 0.281 Chirality : 0.044 0.323 666 Planarity : 0.004 0.032 725 Dihedral : 5.960 50.399 641 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.45 % Allowed : 20.71 % Favored : 74.83 % 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: 0.84 (0.37), residues: 527 helix: 1.32 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.000 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.016 0.001 TYR A 72 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.522 Fit side-chains REVERT: A 72 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8517 (p90) REVERT: A 121 MET cc_start: 0.8929 (ptm) cc_final: 0.8724 (ptp) REVERT: A 370 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 384 LEU cc_start: 0.7394 (pp) cc_final: 0.6783 (mp) REVERT: A 402 GLU cc_start: 0.7772 (tp30) cc_final: 0.7504 (tp30) REVERT: A 481 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 566 ARG cc_start: 0.6969 (mtp85) cc_final: 0.6609 (mtt-85) REVERT: A 572 GLN cc_start: 0.5989 (OUTLIER) cc_final: 0.5780 (mm110) outliers start: 20 outliers final: 11 residues processed: 75 average time/residue: 0.9175 time to fit residues: 72.2965 Evaluate side-chains 70 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 50 optimal weight: 0.0570 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4393 Z= 0.188 Angle : 0.541 8.322 5982 Z= 0.280 Chirality : 0.044 0.273 666 Planarity : 0.004 0.033 725 Dihedral : 5.210 31.414 641 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.90 % Allowed : 21.16 % Favored : 73.94 % 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: 0.85 (0.37), residues: 527 helix: 1.34 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.018 0.002 TYR A 72 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.479 Fit side-chains REVERT: A 72 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8514 (p90) REVERT: A 370 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 402 GLU cc_start: 0.7788 (tp30) cc_final: 0.7511 (tp30) REVERT: A 481 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 566 ARG cc_start: 0.6867 (mtp85) cc_final: 0.6584 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 73 average time/residue: 0.9318 time to fit residues: 71.4658 Evaluate side-chains 67 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4393 Z= 0.155 Angle : 0.504 7.290 5982 Z= 0.263 Chirality : 0.042 0.258 666 Planarity : 0.004 0.032 725 Dihedral : 4.749 30.769 641 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.90 % Allowed : 20.27 % Favored : 74.83 % 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: 1.04 (0.37), residues: 527 helix: 1.49 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.001 0.000 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.015 0.001 TYR A 72 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.481 Fit side-chains REVERT: A 72 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8484 (p90) REVERT: A 419 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7557 (mtt-85) REVERT: A 481 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7656 (t80) outliers start: 22 outliers final: 13 residues processed: 77 average time/residue: 0.9543 time to fit residues: 77.1009 Evaluate side-chains 69 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 50.0000 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8292 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4393 Z= 0.217 Angle : 0.553 7.430 5982 Z= 0.288 Chirality : 0.043 0.245 666 Planarity : 0.004 0.035 725 Dihedral : 4.861 32.320 641 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.57 % Allowed : 20.27 % Favored : 74.16 % 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: 0.96 (0.37), residues: 527 helix: 1.44 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.38 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 0.485 Fit side-chains REVERT: A 72 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8448 (p90) REVERT: A 123 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8592 (tttt) REVERT: A 419 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7690 (mtt-85) REVERT: A 481 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7612 (t80) outliers start: 25 outliers final: 16 residues processed: 75 average time/residue: 0.8774 time to fit residues: 69.0944 Evaluate side-chains 72 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 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: 0.8273 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4393 Z= 0.178 Angle : 0.521 7.311 5982 Z= 0.271 Chirality : 0.042 0.236 666 Planarity : 0.004 0.034 725 Dihedral : 4.703 31.666 641 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.90 % Allowed : 20.49 % Favored : 74.61 % 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: 1.02 (0.37), residues: 527 helix: 1.46 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.30 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.017 0.002 TYR A 72 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.439 Fit side-chains REVERT: A 72 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8357 (p90) REVERT: A 370 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: A 402 GLU cc_start: 0.7780 (tp30) cc_final: 0.7473 (tp30) REVERT: A 419 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7523 (mtt-85) REVERT: A 481 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7680 (t80) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.9395 time to fit residues: 70.8565 Evaluate side-chains 70 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4393 Z= 0.190 Angle : 0.526 7.283 5982 Z= 0.275 Chirality : 0.042 0.228 666 Planarity : 0.004 0.034 725 Dihedral : 4.700 32.069 641 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.45 % Allowed : 20.94 % Favored : 74.61 % 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: 1.01 (0.37), residues: 527 helix: 1.43 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.26 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.018 0.002 TYR A 72 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.483 Fit side-chains REVERT: A 72 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8427 (p90) REVERT: A 197 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: A 370 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A 402 GLU cc_start: 0.7785 (tp30) cc_final: 0.7476 (tp30) REVERT: A 419 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7509 (mtt-85) REVERT: A 481 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7631 (t80) outliers start: 20 outliers final: 15 residues processed: 70 average time/residue: 0.8789 time to fit residues: 64.8206 Evaluate side-chains 70 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4393 Z= 0.184 Angle : 0.518 7.193 5982 Z= 0.271 Chirality : 0.042 0.219 666 Planarity : 0.004 0.034 725 Dihedral : 4.625 32.128 641 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.45 % Allowed : 20.94 % Favored : 74.61 % 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: 1.05 (0.37), residues: 527 helix: 1.45 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.21 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.018 0.002 TYR A 72 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.470 Fit side-chains REVERT: A 72 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8396 (p90) REVERT: A 370 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: A 402 GLU cc_start: 0.7783 (tp30) cc_final: 0.7478 (tp30) REVERT: A 415 LEU cc_start: 0.8264 (tp) cc_final: 0.7965 (tp) REVERT: A 419 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7521 (mtt-85) REVERT: A 481 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7680 (t80) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.9428 time to fit residues: 68.4313 Evaluate side-chains 68 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 overall best weight: 0.2404 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4393 Z= 0.132 Angle : 0.492 6.961 5982 Z= 0.255 Chirality : 0.041 0.249 666 Planarity : 0.004 0.031 725 Dihedral : 4.241 31.167 641 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.56 % Allowed : 22.05 % Favored : 74.39 % 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: 1.33 (0.37), residues: 527 helix: 1.70 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 532 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.001 PHE A 398 TYR 0.015 0.001 TYR A 554 ARG 0.003 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.503 Fit side-chains REVERT: A 415 LEU cc_start: 0.8128 (tp) cc_final: 0.7856 (tp) REVERT: A 419 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7488 (mtt-85) REVERT: A 481 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7610 (t80) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 0.8155 time to fit residues: 62.0614 Evaluate side-chains 66 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.120705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.092269 restraints weight = 4549.966| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.46 r_work: 0.2890 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4393 Z= 0.178 Angle : 0.530 7.101 5982 Z= 0.277 Chirality : 0.043 0.236 666 Planarity : 0.004 0.034 725 Dihedral : 4.429 32.395 641 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 23.16 % Favored : 73.94 % 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: 1.24 (0.37), residues: 527 helix: 1.62 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.15 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.001 0.001 HIS A 313 PHE 0.029 0.002 PHE A 398 TYR 0.017 0.002 TYR A 72 ARG 0.002 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.75 seconds wall clock time: 33 minutes 27.35 seconds (2007.35 seconds total)