Starting phenix.real_space_refine on Fri Aug 2 20:37:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw1_38727/08_2024/8xw1_38727.cif" } resolution = 4.49 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= 0.006 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3378 2.51 5 N 826 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5082 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5082 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 4.48, per 1000 atoms: 0.88 Number of scatterers: 5082 At special positions: 0 Unit cell: (92.13, 87.15, 99.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 854 8.00 N 826 7.00 C 3378 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 77.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.599A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.504A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.835A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 119 removed outlier: 4.175A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 194 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 314 through 319 removed outlier: 6.155A pdb=" N LYS A 317 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.559A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.708A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 440 removed outlier: 3.952A pdb=" N GLN A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 4.544A pdb=" N PHE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 477 through 490 removed outlier: 4.486A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 553 through 559 removed outlier: 4.381A pdb=" N GLU A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 589 through 612 removed outlier: 4.316A pdb=" N PHE A 593 " --> pdb=" O MET A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 646 Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.717A pdb=" N LEU A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 677 removed outlier: 4.095A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 3.539A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 238 removed outlier: 3.902A pdb=" N THR A 235 " --> pdb=" O SER A 326 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 999 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: 2.02 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1541 1.34 - 1.46: 994 1.46 - 1.57: 2649 1.57 - 1.69: 1 1.69 - 1.81: 44 Bond restraints: 5229 Sorted by residual: bond pdb=" CG PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 1.503 1.421 0.082 3.40e-02 8.65e+02 5.81e+00 bond pdb=" CB PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.83e+00 bond pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CG LEU A 120 " pdb=" CD2 LEU A 120 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" C TRP A 335 " pdb=" O TRP A 335 " ideal model delta sigma weight residual 1.236 1.221 0.015 1.15e-02 7.56e+03 1.74e+00 ... (remaining 5224 not shown) Histogram of bond angle deviations from ideal: 96.34 - 103.90: 96 103.90 - 111.46: 2321 111.46 - 119.02: 1857 119.02 - 126.57: 2740 126.57 - 134.13: 99 Bond angle restraints: 7113 Sorted by residual: angle pdb=" N LYS A 503 " pdb=" CA LYS A 503 " pdb=" C LYS A 503 " ideal model delta sigma weight residual 112.88 106.35 6.53 1.29e+00 6.01e-01 2.56e+01 angle pdb=" N PRO A 77 " pdb=" CD PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 103.20 96.34 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 112.00 105.67 6.33 1.40e+00 5.10e-01 2.04e+01 angle pdb=" C PHE A 109 " pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta sigma weight residual 119.83 116.17 3.66 1.11e+00 8.12e-01 1.09e+01 angle pdb=" C ASP A 552 " pdb=" N LYS A 553 " pdb=" CA LYS A 553 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 ... (remaining 7108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2764 16.55 - 33.10: 239 33.10 - 49.65: 42 49.65 - 66.21: 9 66.21 - 82.76: 11 Dihedral angle restraints: 3065 sinusoidal: 1194 harmonic: 1871 Sorted by residual: dihedral pdb=" CA PHE A 440 " pdb=" C PHE A 440 " pdb=" N LEU A 441 " pdb=" CA LEU A 441 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN A 340 " pdb=" C GLN A 340 " pdb=" N GLN A 341 " pdb=" CA GLN A 341 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA MET A 82 " pdb=" C MET A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 587 0.045 - 0.091: 165 0.091 - 0.136: 43 0.136 - 0.181: 4 0.181 - 0.226: 2 Chirality restraints: 801 Sorted by residual: chirality pdb=" CB VAL A 119 " pdb=" CA VAL A 119 " pdb=" CG1 VAL A 119 " pdb=" CG2 VAL A 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 536 " pdb=" N LYS A 536 " pdb=" C LYS A 536 " pdb=" CB LYS A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA GLU A 311 " pdb=" N GLU A 311 " pdb=" C GLU A 311 " pdb=" CB GLU A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 798 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 76 " 0.047 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO A 77 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 307 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C LYS A 307 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS A 307 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 308 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 352 " 0.015 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP A 352 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 352 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 352 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 352 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 352 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 352 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 352 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 352 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 352 " 0.006 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 144 2.69 - 3.24: 5891 3.24 - 3.80: 8715 3.80 - 4.35: 10301 4.35 - 4.90: 16226 Nonbonded interactions: 41277 Sorted by model distance: nonbonded pdb=" O PRO A 354 " pdb=" OH TYR A 712 " model vdw 2.139 3.040 nonbonded pdb=" OE1 GLU A 78 " pdb=" NZ LYS A 81 " model vdw 2.178 3.120 nonbonded pdb=" O PHE A 224 " pdb=" ND2 ASN A 228 " model vdw 2.215 3.120 nonbonded pdb=" O TRP A 335 " pdb=" OG1 THR A 339 " model vdw 2.221 3.040 nonbonded pdb=" O LEU A 635 " pdb=" OG SER A 638 " model vdw 2.234 3.040 ... (remaining 41272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 22.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 5229 Z= 0.332 Angle : 0.821 7.921 7113 Z= 0.465 Chirality : 0.046 0.226 801 Planarity : 0.005 0.068 882 Dihedral : 14.015 82.757 1849 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.19 % Allowed : 0.95 % Favored : 98.87 % 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: -0.07 (0.33), residues: 624 helix: 0.75 (0.25), residues: 417 sheet: -2.19 (1.07), residues: 16 loop : -1.55 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 352 HIS 0.004 0.001 HIS A 229 PHE 0.023 0.002 PHE A 437 TYR 0.024 0.002 TYR A 469 ARG 0.013 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 38 TYR cc_start: 0.8095 (m-80) cc_final: 0.6785 (m-80) REVERT: A 82 MET cc_start: 0.9014 (tpt) cc_final: 0.8787 (tpp) REVERT: A 109 PHE cc_start: 0.9600 (m-10) cc_final: 0.9385 (m-10) REVERT: A 178 MET cc_start: 0.9286 (ppp) cc_final: 0.9031 (ppp) REVERT: A 180 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9069 (tp30) REVERT: A 262 TYR cc_start: 0.9429 (m-80) cc_final: 0.8995 (m-80) REVERT: A 305 ILE cc_start: 0.9548 (pt) cc_final: 0.9301 (pt) REVERT: A 355 GLU cc_start: 0.9432 (tp30) cc_final: 0.9123 (tp30) REVERT: A 437 PHE cc_start: 0.8999 (m-80) cc_final: 0.8594 (m-80) REVERT: A 440 PHE cc_start: 0.8716 (m-10) cc_final: 0.8451 (t80) REVERT: A 461 GLU cc_start: 0.9164 (tp30) cc_final: 0.8754 (mm-30) REVERT: A 475 ASN cc_start: 0.9007 (m110) cc_final: 0.8642 (m110) REVERT: A 511 MET cc_start: 0.9194 (mmp) cc_final: 0.8965 (mmm) REVERT: A 532 ILE cc_start: 0.9414 (tt) cc_final: 0.9171 (tt) REVERT: A 677 GLU cc_start: 0.8620 (pt0) cc_final: 0.8376 (pt0) REVERT: A 710 ASN cc_start: 0.9388 (m-40) cc_final: 0.9166 (m-40) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1480 time to fit residues: 36.1915 Evaluate side-chains 136 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5229 Z= 0.238 Angle : 0.669 8.112 7113 Z= 0.341 Chirality : 0.043 0.188 801 Planarity : 0.005 0.037 882 Dihedral : 4.742 17.795 680 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.38 % Allowed : 3.40 % Favored : 96.22 % 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: 0.70 (0.35), residues: 624 helix: 1.39 (0.25), residues: 422 sheet: -2.04 (1.09), residues: 16 loop : -1.46 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 352 HIS 0.005 0.001 HIS A 236 PHE 0.029 0.002 PHE A 360 TYR 0.014 0.001 TYR A 98 ARG 0.007 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9331 (m-30) cc_final: 0.9053 (m-30) REVERT: A 38 TYR cc_start: 0.8351 (m-80) cc_final: 0.7242 (m-80) REVERT: A 178 MET cc_start: 0.9254 (ppp) cc_final: 0.9015 (ppp) REVERT: A 180 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9133 (tp30) REVERT: A 262 TYR cc_start: 0.9456 (m-80) cc_final: 0.9068 (m-80) REVERT: A 309 ARG cc_start: 0.8871 (mmp80) cc_final: 0.8533 (mmp80) REVERT: A 355 GLU cc_start: 0.9350 (tp30) cc_final: 0.9093 (tp30) REVERT: A 368 TYR cc_start: 0.8763 (t80) cc_final: 0.8292 (t80) REVERT: A 437 PHE cc_start: 0.8973 (m-80) cc_final: 0.8579 (m-80) REVERT: A 461 GLU cc_start: 0.9295 (tp30) cc_final: 0.8707 (mm-30) REVERT: A 475 ASN cc_start: 0.8993 (m110) cc_final: 0.8577 (m110) REVERT: A 476 VAL cc_start: 0.9421 (t) cc_final: 0.9217 (t) REVERT: A 511 MET cc_start: 0.9190 (mmp) cc_final: 0.8941 (mmm) REVERT: A 532 ILE cc_start: 0.9451 (tt) cc_final: 0.9237 (tt) REVERT: A 540 MET cc_start: 0.9619 (mmp) cc_final: 0.9283 (mmp) REVERT: A 576 TYR cc_start: 0.8679 (m-10) cc_final: 0.8475 (m-10) REVERT: A 613 TYR cc_start: 0.9278 (m-80) cc_final: 0.8689 (m-80) REVERT: A 661 LEU cc_start: 0.9782 (mt) cc_final: 0.9206 (mt) REVERT: A 677 GLU cc_start: 0.8570 (pt0) cc_final: 0.8367 (pt0) REVERT: A 689 MET cc_start: 0.9468 (mmp) cc_final: 0.9265 (mmm) REVERT: A 690 MET cc_start: 0.9349 (mmt) cc_final: 0.8985 (tpt) outliers start: 2 outliers final: 1 residues processed: 180 average time/residue: 0.2076 time to fit residues: 50.8414 Evaluate side-chains 143 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5229 Z= 0.253 Angle : 0.672 12.466 7113 Z= 0.341 Chirality : 0.042 0.177 801 Planarity : 0.005 0.036 882 Dihedral : 4.606 16.836 680 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.19 % Allowed : 3.97 % Favored : 95.84 % 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 (0.35), residues: 624 helix: 1.57 (0.26), residues: 422 sheet: -1.77 (1.16), residues: 16 loop : -1.32 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 624 HIS 0.005 0.001 HIS A 162 PHE 0.022 0.002 PHE A 717 TYR 0.010 0.001 TYR A 98 ARG 0.004 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9346 (m-30) cc_final: 0.9023 (m-30) REVERT: A 262 TYR cc_start: 0.9482 (m-80) cc_final: 0.9278 (m-80) REVERT: A 319 ILE cc_start: 0.9510 (mp) cc_final: 0.8877 (mp) REVERT: A 355 GLU cc_start: 0.9370 (tp30) cc_final: 0.9077 (tp30) REVERT: A 368 TYR cc_start: 0.8612 (t80) cc_final: 0.8395 (t80) REVERT: A 437 PHE cc_start: 0.9026 (m-80) cc_final: 0.8540 (m-80) REVERT: A 445 LEU cc_start: 0.9785 (mt) cc_final: 0.9583 (mt) REVERT: A 475 ASN cc_start: 0.9009 (m110) cc_final: 0.8597 (m110) REVERT: A 511 MET cc_start: 0.9188 (mmp) cc_final: 0.8932 (mmm) REVERT: A 540 MET cc_start: 0.9616 (mmp) cc_final: 0.9276 (mmp) REVERT: A 579 LEU cc_start: 0.9703 (mt) cc_final: 0.9386 (mt) REVERT: A 613 TYR cc_start: 0.9269 (m-80) cc_final: 0.8624 (m-80) REVERT: A 661 LEU cc_start: 0.9649 (mt) cc_final: 0.9438 (mt) REVERT: A 690 MET cc_start: 0.9341 (mmt) cc_final: 0.8982 (tpt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1352 time to fit residues: 31.5536 Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.0010 chunk 60 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5229 Z= 0.170 Angle : 0.621 7.716 7113 Z= 0.314 Chirality : 0.042 0.181 801 Planarity : 0.004 0.038 882 Dihedral : 4.393 17.691 680 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 0.92 (0.35), residues: 624 helix: 1.53 (0.25), residues: 428 sheet: -1.62 (1.17), residues: 16 loop : -1.41 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.005 0.001 HIS A 162 PHE 0.019 0.002 PHE A 428 TYR 0.008 0.001 TYR A 98 ARG 0.002 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9342 (m-30) cc_final: 0.8970 (m-30) REVERT: A 180 GLU cc_start: 0.9078 (tp30) cc_final: 0.8716 (tp30) REVERT: A 399 LEU cc_start: 0.9739 (mt) cc_final: 0.9449 (mt) REVERT: A 437 PHE cc_start: 0.9063 (m-80) cc_final: 0.8613 (m-80) REVERT: A 452 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 461 GLU cc_start: 0.9295 (tp30) cc_final: 0.8778 (mm-30) REVERT: A 476 VAL cc_start: 0.9407 (t) cc_final: 0.9201 (t) REVERT: A 511 MET cc_start: 0.9190 (mmp) cc_final: 0.8943 (mmm) REVERT: A 540 MET cc_start: 0.9578 (mmp) cc_final: 0.9270 (mmp) REVERT: A 613 TYR cc_start: 0.9146 (m-80) cc_final: 0.8464 (m-80) REVERT: A 677 GLU cc_start: 0.8629 (pt0) cc_final: 0.8399 (pt0) REVERT: A 682 ARG cc_start: 0.8546 (mpt-90) cc_final: 0.8058 (ttm110) REVERT: A 690 MET cc_start: 0.9313 (mmt) cc_final: 0.8914 (tpt) REVERT: A 710 ASN cc_start: 0.9247 (m-40) cc_final: 0.9029 (m-40) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1337 time to fit residues: 32.4023 Evaluate side-chains 140 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.0670 chunk 31 optimal weight: 0.0570 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 615 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5229 Z= 0.176 Angle : 0.635 8.954 7113 Z= 0.320 Chirality : 0.041 0.177 801 Planarity : 0.004 0.039 882 Dihedral : 4.347 18.464 680 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: 0.90 (0.35), residues: 624 helix: 1.47 (0.25), residues: 436 sheet: -1.78 (1.35), residues: 11 loop : -1.43 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 75 HIS 0.005 0.001 HIS A 162 PHE 0.018 0.001 PHE A 428 TYR 0.009 0.001 TYR A 98 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9339 (m-30) cc_final: 0.8961 (m-30) REVERT: A 165 MET cc_start: 0.9359 (mmp) cc_final: 0.9098 (mmp) REVERT: A 180 GLU cc_start: 0.9096 (tp30) cc_final: 0.8761 (tp30) REVERT: A 262 TYR cc_start: 0.9462 (m-80) cc_final: 0.9165 (m-80) REVERT: A 297 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9050 (mm-30) REVERT: A 298 ILE cc_start: 0.9663 (mm) cc_final: 0.9459 (pt) REVERT: A 399 LEU cc_start: 0.9728 (mt) cc_final: 0.9433 (mt) REVERT: A 437 PHE cc_start: 0.9071 (m-80) cc_final: 0.8218 (m-80) REVERT: A 445 LEU cc_start: 0.9762 (mt) cc_final: 0.9551 (mt) REVERT: A 461 GLU cc_start: 0.9325 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 511 MET cc_start: 0.9148 (mmp) cc_final: 0.8892 (mmm) REVERT: A 540 MET cc_start: 0.9566 (mmp) cc_final: 0.9265 (mmp) REVERT: A 677 GLU cc_start: 0.8624 (pt0) cc_final: 0.8407 (pt0) REVERT: A 682 ARG cc_start: 0.8573 (mpt-90) cc_final: 0.8064 (ttm110) REVERT: A 689 MET cc_start: 0.9454 (mmp) cc_final: 0.9251 (mmm) REVERT: A 690 MET cc_start: 0.9325 (mmt) cc_final: 0.8913 (tpt) REVERT: A 710 ASN cc_start: 0.9224 (m-40) cc_final: 0.9006 (m-40) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1393 time to fit residues: 33.4031 Evaluate side-chains 133 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 615 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5229 Z= 0.170 Angle : 0.609 7.477 7113 Z= 0.305 Chirality : 0.041 0.179 801 Planarity : 0.004 0.042 882 Dihedral : 4.235 18.304 680 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.19 % Allowed : 2.46 % Favored : 97.35 % 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: 1.01 (0.35), residues: 624 helix: 1.51 (0.25), residues: 437 sheet: -1.65 (1.49), residues: 10 loop : -1.30 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 624 HIS 0.005 0.001 HIS A 162 PHE 0.017 0.001 PHE A 428 TYR 0.007 0.001 TYR A 613 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9337 (m-30) cc_final: 0.8947 (m-30) REVERT: A 165 MET cc_start: 0.9350 (mmp) cc_final: 0.9080 (mmp) REVERT: A 180 GLU cc_start: 0.9135 (tp30) cc_final: 0.8790 (tp30) REVERT: A 262 TYR cc_start: 0.9497 (m-80) cc_final: 0.9167 (m-80) REVERT: A 298 ILE cc_start: 0.9662 (mm) cc_final: 0.9450 (pt) REVERT: A 437 PHE cc_start: 0.9087 (m-80) cc_final: 0.8212 (m-80) REVERT: A 445 LEU cc_start: 0.9761 (mt) cc_final: 0.9549 (mt) REVERT: A 452 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 461 GLU cc_start: 0.9321 (tp30) cc_final: 0.8687 (mm-30) REVERT: A 511 MET cc_start: 0.9141 (mmp) cc_final: 0.8869 (mmm) REVERT: A 540 MET cc_start: 0.9583 (mmp) cc_final: 0.9279 (mmp) REVERT: A 579 LEU cc_start: 0.9676 (mt) cc_final: 0.9471 (mt) REVERT: A 613 TYR cc_start: 0.8916 (m-80) cc_final: 0.8320 (m-80) REVERT: A 682 ARG cc_start: 0.8583 (mpt-90) cc_final: 0.8093 (ttm110) REVERT: A 690 MET cc_start: 0.9307 (mmt) cc_final: 0.8899 (tpt) REVERT: A 710 ASN cc_start: 0.9228 (m-40) cc_final: 0.9017 (m-40) outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.1286 time to fit residues: 30.1016 Evaluate side-chains 128 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5229 Z= 0.190 Angle : 0.640 7.888 7113 Z= 0.320 Chirality : 0.041 0.175 801 Planarity : 0.004 0.042 882 Dihedral : 4.274 17.612 680 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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 (0.35), residues: 624 helix: 1.70 (0.26), residues: 426 sheet: -1.65 (1.48), residues: 10 loop : -1.08 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 75 HIS 0.005 0.001 HIS A 628 PHE 0.017 0.001 PHE A 428 TYR 0.010 0.001 TYR A 613 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9339 (m-30) cc_final: 0.8968 (m-30) REVERT: A 76 MET cc_start: 0.9557 (mmm) cc_final: 0.9252 (mmm) REVERT: A 97 VAL cc_start: 0.9701 (t) cc_final: 0.9459 (p) REVERT: A 165 MET cc_start: 0.9358 (mmp) cc_final: 0.9082 (mmp) REVERT: A 180 GLU cc_start: 0.9160 (tp30) cc_final: 0.8829 (tp30) REVERT: A 262 TYR cc_start: 0.9505 (m-80) cc_final: 0.8937 (m-80) REVERT: A 298 ILE cc_start: 0.9643 (mm) cc_final: 0.9396 (pt) REVERT: A 437 PHE cc_start: 0.9099 (m-80) cc_final: 0.8188 (m-80) REVERT: A 445 LEU cc_start: 0.9758 (mt) cc_final: 0.9531 (mt) REVERT: A 448 MET cc_start: 0.9424 (mmm) cc_final: 0.9179 (tpt) REVERT: A 452 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 461 GLU cc_start: 0.9298 (tp30) cc_final: 0.8983 (tp30) REVERT: A 511 MET cc_start: 0.9151 (mmp) cc_final: 0.8866 (mmm) REVERT: A 540 MET cc_start: 0.9602 (mmp) cc_final: 0.9289 (mmp) REVERT: A 579 LEU cc_start: 0.9691 (mt) cc_final: 0.9415 (mt) REVERT: A 613 TYR cc_start: 0.9035 (m-80) cc_final: 0.8399 (m-80) REVERT: A 682 ARG cc_start: 0.8612 (mpt-90) cc_final: 0.8095 (ttm110) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1314 time to fit residues: 30.2351 Evaluate side-chains 129 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN A 426 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5229 Z= 0.167 Angle : 0.622 7.865 7113 Z= 0.311 Chirality : 0.042 0.195 801 Planarity : 0.005 0.046 882 Dihedral : 4.191 17.486 680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 624 helix: 1.51 (0.25), residues: 436 sheet: -1.49 (1.48), residues: 10 loop : -1.20 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.005 0.001 HIS A 162 PHE 0.017 0.001 PHE A 428 TYR 0.015 0.001 TYR A 469 ARG 0.007 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9314 (m-30) cc_final: 0.8537 (t0) REVERT: A 76 MET cc_start: 0.9495 (mmm) cc_final: 0.9200 (mmm) REVERT: A 82 MET cc_start: 0.9059 (tpt) cc_final: 0.8817 (tpp) REVERT: A 97 VAL cc_start: 0.9668 (t) cc_final: 0.9449 (p) REVERT: A 165 MET cc_start: 0.9347 (mmp) cc_final: 0.9071 (mmp) REVERT: A 180 GLU cc_start: 0.9090 (tp30) cc_final: 0.8793 (tp30) REVERT: A 262 TYR cc_start: 0.9496 (m-80) cc_final: 0.8948 (m-80) REVERT: A 358 ASP cc_start: 0.8978 (t70) cc_final: 0.8563 (t0) REVERT: A 437 PHE cc_start: 0.9126 (m-10) cc_final: 0.8242 (m-80) REVERT: A 452 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 461 GLU cc_start: 0.9278 (tp30) cc_final: 0.8984 (tp30) REVERT: A 469 TYR cc_start: 0.9465 (t80) cc_final: 0.9030 (t80) REVERT: A 511 MET cc_start: 0.9126 (mmp) cc_final: 0.8813 (mmm) REVERT: A 535 LEU cc_start: 0.9627 (mt) cc_final: 0.9260 (mt) REVERT: A 539 ILE cc_start: 0.9700 (mm) cc_final: 0.9489 (mm) REVERT: A 540 MET cc_start: 0.9595 (mmp) cc_final: 0.9260 (mmp) REVERT: A 570 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9219 (tm-30) REVERT: A 579 LEU cc_start: 0.9694 (mt) cc_final: 0.9430 (mt) REVERT: A 613 TYR cc_start: 0.8937 (m-80) cc_final: 0.8259 (m-80) REVERT: A 682 ARG cc_start: 0.8586 (mpt-90) cc_final: 0.8078 (ttm110) REVERT: A 690 MET cc_start: 0.9316 (mmt) cc_final: 0.8878 (tpt) REVERT: A 710 ASN cc_start: 0.9179 (m-40) cc_final: 0.8970 (m-40) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1468 time to fit residues: 34.6458 Evaluate side-chains 126 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 397 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5229 Z= 0.174 Angle : 0.646 8.122 7113 Z= 0.321 Chirality : 0.042 0.171 801 Planarity : 0.005 0.045 882 Dihedral : 4.147 17.345 680 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 (0.35), residues: 624 helix: 1.32 (0.25), residues: 443 sheet: -1.42 (1.47), residues: 10 loop : -1.26 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.006 0.001 HIS A 162 PHE 0.018 0.001 PHE A 19 TYR 0.008 0.001 TYR A 613 ARG 0.005 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9292 (m-30) cc_final: 0.8626 (t0) REVERT: A 82 MET cc_start: 0.9065 (tpt) cc_final: 0.8818 (tpp) REVERT: A 165 MET cc_start: 0.9346 (mmp) cc_final: 0.9073 (mmp) REVERT: A 180 GLU cc_start: 0.9083 (tp30) cc_final: 0.8812 (tp30) REVERT: A 262 TYR cc_start: 0.9485 (m-80) cc_final: 0.8941 (m-80) REVERT: A 298 ILE cc_start: 0.9590 (mm) cc_final: 0.9324 (pt) REVERT: A 389 PHE cc_start: 0.9019 (m-80) cc_final: 0.8795 (m-80) REVERT: A 437 PHE cc_start: 0.9105 (m-10) cc_final: 0.8210 (m-80) REVERT: A 445 LEU cc_start: 0.9716 (mt) cc_final: 0.9493 (mt) REVERT: A 448 MET cc_start: 0.9403 (mmm) cc_final: 0.9195 (tpt) REVERT: A 452 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 461 GLU cc_start: 0.9264 (tp30) cc_final: 0.8951 (tp30) REVERT: A 469 TYR cc_start: 0.9433 (t80) cc_final: 0.9031 (t80) REVERT: A 511 MET cc_start: 0.9151 (mmp) cc_final: 0.8826 (mmm) REVERT: A 539 ILE cc_start: 0.9711 (mm) cc_final: 0.9504 (mm) REVERT: A 540 MET cc_start: 0.9579 (mmp) cc_final: 0.9234 (mmp) REVERT: A 570 GLU cc_start: 0.9597 (tm-30) cc_final: 0.9253 (tm-30) REVERT: A 579 LEU cc_start: 0.9699 (mt) cc_final: 0.9439 (mt) REVERT: A 613 TYR cc_start: 0.8922 (m-80) cc_final: 0.8226 (m-80) REVERT: A 677 GLU cc_start: 0.8643 (pt0) cc_final: 0.8422 (pt0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1276 time to fit residues: 30.3214 Evaluate side-chains 129 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5229 Z= 0.189 Angle : 0.668 8.361 7113 Z= 0.338 Chirality : 0.042 0.181 801 Planarity : 0.004 0.047 882 Dihedral : 4.151 17.142 680 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.76 (0.35), residues: 624 helix: 1.27 (0.25), residues: 443 sheet: -1.35 (1.47), residues: 10 loop : -1.38 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.006 0.001 HIS A 162 PHE 0.021 0.001 PHE A 19 TYR 0.018 0.001 TYR A 181 ARG 0.003 0.000 ARG A 682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9290 (m-30) cc_final: 0.8643 (t0) REVERT: A 82 MET cc_start: 0.9043 (tpt) cc_final: 0.8797 (tpp) REVERT: A 98 TYR cc_start: 0.8800 (t80) cc_final: 0.8545 (t80) REVERT: A 165 MET cc_start: 0.9347 (mmp) cc_final: 0.9069 (mmp) REVERT: A 180 GLU cc_start: 0.8924 (tp30) cc_final: 0.8660 (tp30) REVERT: A 262 TYR cc_start: 0.9487 (m-80) cc_final: 0.8945 (m-80) REVERT: A 320 MET cc_start: 0.8628 (tpt) cc_final: 0.8147 (ttt) REVERT: A 358 ASP cc_start: 0.9018 (t70) cc_final: 0.8660 (t0) REVERT: A 437 PHE cc_start: 0.9101 (m-10) cc_final: 0.8206 (m-80) REVERT: A 445 LEU cc_start: 0.9713 (mt) cc_final: 0.9487 (mt) REVERT: A 448 MET cc_start: 0.9393 (mmm) cc_final: 0.9190 (tpt) REVERT: A 452 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 461 GLU cc_start: 0.9250 (tp30) cc_final: 0.8933 (tp30) REVERT: A 469 TYR cc_start: 0.9463 (t80) cc_final: 0.9146 (t80) REVERT: A 511 MET cc_start: 0.9128 (mmp) cc_final: 0.8810 (mmm) REVERT: A 539 ILE cc_start: 0.9709 (mm) cc_final: 0.9499 (mm) REVERT: A 540 MET cc_start: 0.9580 (mmp) cc_final: 0.9229 (mmp) REVERT: A 579 LEU cc_start: 0.9702 (mt) cc_final: 0.9423 (mt) REVERT: A 613 TYR cc_start: 0.8894 (m-80) cc_final: 0.8210 (m-80) REVERT: A 710 ASN cc_start: 0.9162 (m-40) cc_final: 0.8924 (m-40) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1261 time to fit residues: 30.1368 Evaluate side-chains 126 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 0.0270 chunk 57 optimal weight: 0.0050 chunk 33 optimal weight: 3.9990 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064762 restraints weight = 17033.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.067393 restraints weight = 9682.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069198 restraints weight = 6461.193| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5229 Z= 0.182 Angle : 0.669 8.245 7113 Z= 0.337 Chirality : 0.042 0.176 801 Planarity : 0.004 0.048 882 Dihedral : 4.120 17.390 680 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.83 (0.35), residues: 624 helix: 1.35 (0.25), residues: 437 sheet: -1.26 (1.47), residues: 10 loop : -1.31 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.008 0.001 HIS A 628 PHE 0.019 0.001 PHE A 19 TYR 0.008 0.001 TYR A 613 ARG 0.002 0.000 ARG A 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.80 seconds wall clock time: 27 minutes 31.70 seconds (1651.70 seconds total)