Starting phenix.real_space_refine on Mon Mar 11 01:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/03_2024/7wxi_32880_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 4064 2.51 5 N 1174 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.65 Number of scatterers: 6522 At special positions: 0 Unit cell: (98.58, 92.22, 62.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1252 8.00 N 1174 7.00 C 4064 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: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP A 801 " pdb=" CB RGP B 801 " Number of C-beta restraints generated: 1596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 42.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 349 through 364 removed outlier: 4.096A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'B' and resid 349 through 364 removed outlier: 4.096A pdb=" N ALA B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 432 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 740 through 743 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing sheet with id= A, first strand: chain 'A' and resid 455 through 458 Processing sheet with id= B, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 605 through 607 removed outlier: 7.626A pdb=" N GLU A 662 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 443 through 447 removed outlier: 6.945A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 455 through 458 Processing sheet with id= F, first strand: chain 'B' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 605 through 607 removed outlier: 7.626A pdb=" N GLU B 662 " --> pdb=" O ILE B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.945A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 684 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: 1.73 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1140 1.31 - 1.43: 1536 1.43 - 1.56: 3896 1.56 - 1.68: 2 1.68 - 1.81: 46 Bond restraints: 6620 Sorted by residual: bond pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.25e-02 6.40e+03 3.13e+00 ... (remaining 6615 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 184 106.52 - 113.39: 3874 113.39 - 120.26: 2292 120.26 - 127.12: 2554 127.12 - 133.99: 60 Bond angle restraints: 8964 Sorted by residual: angle pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " pdb=" OA3 RGP B 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " pdb=" OA3 RGP A 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CG RGP B 801 " pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CG RGP A 801 " pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N ARG A 544 " pdb=" CA ARG A 544 " pdb=" C ARG A 544 " ideal model delta sigma weight residual 114.75 111.53 3.22 1.26e+00 6.30e-01 6.53e+00 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 3506 16.01 - 32.02: 416 32.02 - 48.02: 98 48.02 - 64.03: 18 64.03 - 80.04: 14 Dihedral angle restraints: 4052 sinusoidal: 1588 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ILE A 732 " pdb=" C ILE A 732 " pdb=" N HIS A 733 " pdb=" CA HIS A 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE B 732 " pdb=" C ILE B 732 " pdb=" N HIS B 733 " pdb=" CA HIS B 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 366 " pdb=" C THR A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta harmonic sigma weight residual 180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 562 0.030 - 0.059: 276 0.059 - 0.089: 136 0.089 - 0.118: 52 0.118 - 0.148: 22 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE B 574 " pdb=" N ILE B 574 " pdb=" C ILE B 574 " pdb=" CB ILE B 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 519 " pdb=" N VAL B 519 " pdb=" C VAL B 519 " pdb=" CB VAL B 519 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1045 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 644 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 644 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 664 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 665 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.018 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 372 2.70 - 3.25: 7752 3.25 - 3.80: 10467 3.80 - 4.35: 12480 4.35 - 4.90: 20263 Nonbonded interactions: 51334 Sorted by model distance: nonbonded pdb=" O ILE A 429 " pdb=" OG SER A 433 " model vdw 2.148 2.440 nonbonded pdb=" O ILE B 429 " pdb=" OG SER B 433 " model vdw 2.148 2.440 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.181 2.440 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.181 2.440 nonbonded pdb=" O CYS B 570 " pdb=" ND1 HIS B 571 " model vdw 2.224 2.520 ... (remaining 51329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.160 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: 5.660 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 23.050 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.008 0.152 6620 Z= 0.520 Angle : 0.875 11.589 8964 Z= 0.460 Chirality : 0.046 0.148 1048 Planarity : 0.005 0.043 1174 Dihedral : 15.473 80.038 2456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.22 % Favored : 81.78 % Rotamer: Outliers : 0.58 % Allowed : 11.88 % Favored : 87.54 % 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: -4.77 (0.24), residues: 856 helix: -2.25 (0.22), residues: 354 sheet: -4.26 (0.37), residues: 112 loop : -3.68 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 748 HIS 0.007 0.002 HIS A 733 PHE 0.009 0.002 PHE B 387 TYR 0.011 0.002 TYR A 654 ARG 0.006 0.001 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8727 (t80) cc_final: 0.8397 (t80) REVERT: A 396 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (pp) REVERT: A 487 LEU cc_start: 0.8871 (tp) cc_final: 0.8670 (tp) REVERT: A 505 LEU cc_start: 0.7996 (mt) cc_final: 0.7767 (mt) REVERT: A 534 MET cc_start: 0.8501 (tmm) cc_final: 0.7827 (tmm) REVERT: A 575 ASP cc_start: 0.8038 (t70) cc_final: 0.7835 (t70) REVERT: A 577 ASP cc_start: 0.8501 (t70) cc_final: 0.8147 (t70) REVERT: B 387 PHE cc_start: 0.8717 (t80) cc_final: 0.8386 (t80) REVERT: B 505 LEU cc_start: 0.8076 (mt) cc_final: 0.7842 (mt) REVERT: B 534 MET cc_start: 0.8501 (tmm) cc_final: 0.7814 (tmm) REVERT: B 673 HIS cc_start: 0.8915 (t-90) cc_final: 0.8711 (t-170) outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.2235 time to fit residues: 39.1724 Evaluate side-chains 94 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 369 GLN A 400 GLN A 454 GLN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 770 HIS B 354 ASN B 369 GLN B 400 GLN B 454 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 770 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6620 Z= 0.194 Angle : 0.636 7.375 8964 Z= 0.326 Chirality : 0.044 0.169 1048 Planarity : 0.005 0.038 1174 Dihedral : 5.455 37.489 934 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.29 % Allowed : 6.96 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.27), residues: 856 helix: -0.28 (0.26), residues: 364 sheet: -3.42 (0.41), residues: 114 loop : -3.25 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 768 HIS 0.007 0.001 HIS A 733 PHE 0.017 0.002 PHE A 760 TYR 0.007 0.001 TYR A 573 ARG 0.004 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7865 (mpp) cc_final: 0.7416 (mpp) REVERT: A 354 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 387 PHE cc_start: 0.8429 (t80) cc_final: 0.8219 (t80) REVERT: A 487 LEU cc_start: 0.8580 (tp) cc_final: 0.8322 (tp) REVERT: A 505 LEU cc_start: 0.8209 (mt) cc_final: 0.7838 (mt) REVERT: A 577 ASP cc_start: 0.8259 (t70) cc_final: 0.7943 (t70) REVERT: A 672 ASN cc_start: 0.8996 (m110) cc_final: 0.8752 (m110) REVERT: B 351 MET cc_start: 0.7906 (mpp) cc_final: 0.7464 (mpp) REVERT: B 353 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8914 (mm-30) REVERT: B 354 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 387 PHE cc_start: 0.8427 (t80) cc_final: 0.8181 (t80) REVERT: B 505 LEU cc_start: 0.8234 (mt) cc_final: 0.7866 (mt) REVERT: B 651 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8539 (mtpt) REVERT: B 662 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6903 (mm-30) REVERT: B 672 ASN cc_start: 0.9018 (m110) cc_final: 0.8818 (m110) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.1490 time to fit residues: 30.4258 Evaluate side-chains 113 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6620 Z= 0.176 Angle : 0.625 8.323 8964 Z= 0.313 Chirality : 0.041 0.158 1048 Planarity : 0.005 0.038 1174 Dihedral : 5.106 36.433 934 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.28), residues: 856 helix: 0.59 (0.27), residues: 364 sheet: -2.80 (0.41), residues: 116 loop : -2.89 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 768 HIS 0.004 0.001 HIS A 733 PHE 0.013 0.002 PHE A 760 TYR 0.011 0.001 TYR B 654 ARG 0.007 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7966 (mpp) cc_final: 0.7535 (mpp) REVERT: A 487 LEU cc_start: 0.8531 (tp) cc_final: 0.8327 (tp) REVERT: A 534 MET cc_start: 0.8533 (tmm) cc_final: 0.8218 (tmm) REVERT: A 601 MET cc_start: 0.8225 (tmm) cc_final: 0.8010 (tmm) REVERT: B 351 MET cc_start: 0.8029 (mpp) cc_final: 0.7585 (mpp) REVERT: B 534 MET cc_start: 0.8535 (tmm) cc_final: 0.8194 (tmm) REVERT: B 651 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8523 (mtpt) REVERT: B 662 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6894 (mm-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1534 time to fit residues: 32.8637 Evaluate side-chains 116 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 499 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 499 ASN ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6620 Z= 0.187 Angle : 0.627 9.141 8964 Z= 0.309 Chirality : 0.043 0.349 1048 Planarity : 0.004 0.037 1174 Dihedral : 5.022 35.854 934 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -1.75 (0.28), residues: 856 helix: 0.77 (0.27), residues: 362 sheet: -2.56 (0.42), residues: 116 loop : -2.71 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 768 HIS 0.003 0.001 HIS A 681 PHE 0.020 0.002 PHE B 616 TYR 0.009 0.001 TYR A 654 ARG 0.007 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.9103 (pt) cc_final: 0.8875 (pt) REVERT: A 412 LEU cc_start: 0.8791 (mm) cc_final: 0.8502 (mm) REVERT: A 516 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6203 (tm-30) REVERT: A 526 GLU cc_start: 0.7450 (mp0) cc_final: 0.6780 (mp0) REVERT: A 534 MET cc_start: 0.8341 (tmm) cc_final: 0.8004 (tmm) REVERT: A 577 ASP cc_start: 0.8246 (t0) cc_final: 0.7909 (t70) REVERT: A 672 ASN cc_start: 0.8871 (m110) cc_final: 0.8603 (m110) REVERT: B 351 MET cc_start: 0.8030 (mpp) cc_final: 0.7620 (mpp) REVERT: B 412 LEU cc_start: 0.8812 (mm) cc_final: 0.8540 (mm) REVERT: B 534 MET cc_start: 0.8364 (tmm) cc_final: 0.8044 (tmm) REVERT: B 651 LYS cc_start: 0.8840 (tmtt) cc_final: 0.8527 (mtpt) REVERT: B 672 ASN cc_start: 0.8857 (m110) cc_final: 0.8611 (m110) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1452 time to fit residues: 32.3191 Evaluate side-chains 126 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6620 Z= 0.200 Angle : 0.623 8.653 8964 Z= 0.310 Chirality : 0.042 0.172 1048 Planarity : 0.004 0.039 1174 Dihedral : 4.968 35.078 934 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -1.57 (0.28), residues: 856 helix: 0.88 (0.27), residues: 368 sheet: -2.65 (0.42), residues: 106 loop : -2.57 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 748 HIS 0.003 0.001 HIS A 733 PHE 0.009 0.001 PHE A 760 TYR 0.009 0.001 TYR A 573 ARG 0.002 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7252 (mpp) cc_final: 0.6827 (mpp) REVERT: A 489 LEU cc_start: 0.8744 (mp) cc_final: 0.8381 (mp) REVERT: A 516 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6115 (tm-30) REVERT: A 672 ASN cc_start: 0.8849 (m110) cc_final: 0.8570 (m110) REVERT: B 351 MET cc_start: 0.7328 (mpp) cc_final: 0.6882 (mpp) REVERT: B 615 ILE cc_start: 0.9533 (tp) cc_final: 0.9323 (mm) REVERT: B 651 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8580 (tmtt) REVERT: B 662 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6929 (mm-30) REVERT: B 672 ASN cc_start: 0.8859 (m110) cc_final: 0.8583 (m110) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1534 time to fit residues: 32.2048 Evaluate side-chains 128 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 369 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6620 Z= 0.179 Angle : 0.620 8.755 8964 Z= 0.306 Chirality : 0.042 0.187 1048 Planarity : 0.005 0.039 1174 Dihedral : 4.964 34.530 934 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -1.42 (0.29), residues: 856 helix: 0.97 (0.28), residues: 368 sheet: -2.68 (0.36), residues: 132 loop : -2.33 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 748 HIS 0.002 0.001 HIS A 733 PHE 0.018 0.001 PHE B 616 TYR 0.007 0.001 TYR A 654 ARG 0.011 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7478 (mpp) cc_final: 0.7136 (mpp) REVERT: A 388 ILE cc_start: 0.9147 (pt) cc_final: 0.8933 (pt) REVERT: A 489 LEU cc_start: 0.8595 (mp) cc_final: 0.8325 (mp) REVERT: A 516 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 622 MET cc_start: 0.8837 (tmm) cc_final: 0.7710 (tmm) REVERT: A 626 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7686 (mp0) REVERT: A 672 ASN cc_start: 0.8832 (m110) cc_final: 0.8559 (m110) REVERT: B 351 MET cc_start: 0.7472 (mpp) cc_final: 0.7118 (mpp) REVERT: B 522 VAL cc_start: 0.9043 (p) cc_final: 0.8705 (p) REVERT: B 662 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 672 ASN cc_start: 0.8879 (m110) cc_final: 0.8663 (m110) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1485 time to fit residues: 31.4460 Evaluate side-chains 126 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.0170 overall best weight: 0.8052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6620 Z= 0.197 Angle : 0.633 9.071 8964 Z= 0.313 Chirality : 0.043 0.235 1048 Planarity : 0.004 0.038 1174 Dihedral : 4.995 34.092 934 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -1.30 (0.29), residues: 856 helix: 1.09 (0.28), residues: 366 sheet: -2.56 (0.37), residues: 132 loop : -2.30 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 748 HIS 0.003 0.001 HIS A 681 PHE 0.009 0.001 PHE A 760 TYR 0.009 0.001 TYR A 654 ARG 0.003 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7503 (mpp) cc_final: 0.7181 (mpp) REVERT: A 362 MET cc_start: 0.8266 (ptp) cc_final: 0.7802 (tpp) REVERT: A 388 ILE cc_start: 0.9151 (pt) cc_final: 0.8945 (pt) REVERT: A 503 MET cc_start: 0.8237 (tpp) cc_final: 0.7902 (tmm) REVERT: A 516 GLU cc_start: 0.6707 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 570 CYS cc_start: 0.8155 (m) cc_final: 0.7940 (m) REVERT: A 615 ILE cc_start: 0.9538 (tp) cc_final: 0.9330 (mm) REVERT: A 622 MET cc_start: 0.8840 (tmm) cc_final: 0.7712 (tmm) REVERT: A 626 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7775 (mp0) REVERT: A 672 ASN cc_start: 0.8869 (m110) cc_final: 0.8648 (m110) REVERT: B 351 MET cc_start: 0.7557 (mpp) cc_final: 0.7223 (mpp) REVERT: B 388 ILE cc_start: 0.9074 (pt) cc_final: 0.8872 (pt) REVERT: B 489 LEU cc_start: 0.8553 (mp) cc_final: 0.8053 (mp) REVERT: B 570 CYS cc_start: 0.8320 (m) cc_final: 0.8113 (m) REVERT: B 662 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 672 ASN cc_start: 0.8860 (m110) cc_final: 0.8656 (m110) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1487 time to fit residues: 30.4490 Evaluate side-chains 119 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.0040 chunk 77 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6620 Z= 0.176 Angle : 0.639 9.312 8964 Z= 0.312 Chirality : 0.043 0.188 1048 Planarity : 0.005 0.038 1174 Dihedral : 4.930 33.689 934 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.21 (0.29), residues: 856 helix: 1.12 (0.28), residues: 364 sheet: -2.42 (0.38), residues: 132 loop : -2.22 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 768 HIS 0.007 0.001 HIS A 733 PHE 0.018 0.001 PHE A 616 TYR 0.008 0.001 TYR B 654 ARG 0.012 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7535 (mpp) cc_final: 0.7153 (mpp) REVERT: A 362 MET cc_start: 0.8238 (ptp) cc_final: 0.7947 (tpp) REVERT: A 503 MET cc_start: 0.8271 (tpp) cc_final: 0.8027 (tmm) REVERT: A 570 CYS cc_start: 0.8199 (m) cc_final: 0.7989 (m) REVERT: A 615 ILE cc_start: 0.9544 (tp) cc_final: 0.9327 (mm) REVERT: A 616 PHE cc_start: 0.8436 (t80) cc_final: 0.8201 (t80) REVERT: A 622 MET cc_start: 0.8833 (tmm) cc_final: 0.7712 (tmm) REVERT: A 626 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7766 (mp0) REVERT: B 351 MET cc_start: 0.7512 (mpp) cc_final: 0.7282 (mpp) REVERT: B 662 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7036 (mm-30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1511 time to fit residues: 30.8230 Evaluate side-chains 118 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.0570 chunk 49 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6620 Z= 0.165 Angle : 0.630 8.933 8964 Z= 0.311 Chirality : 0.042 0.187 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.816 33.285 934 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -1.06 (0.29), residues: 856 helix: 1.10 (0.28), residues: 364 sheet: -2.21 (0.39), residues: 132 loop : -2.03 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 768 HIS 0.006 0.001 HIS A 733 PHE 0.016 0.001 PHE A 616 TYR 0.007 0.001 TYR A 654 ARG 0.005 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7474 (mpp) cc_final: 0.7174 (mpp) REVERT: A 362 MET cc_start: 0.8292 (ptp) cc_final: 0.7806 (tpp) REVERT: A 503 MET cc_start: 0.8234 (tpp) cc_final: 0.7992 (tmm) REVERT: A 672 ASN cc_start: 0.8802 (m110) cc_final: 0.8584 (m110) REVERT: A 690 ASP cc_start: 0.7841 (p0) cc_final: 0.7637 (p0) REVERT: B 351 MET cc_start: 0.7609 (mpp) cc_final: 0.7280 (mpp) REVERT: B 585 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8661 (ttm110) REVERT: B 672 ASN cc_start: 0.8801 (m110) cc_final: 0.8595 (m110) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1685 time to fit residues: 34.8270 Evaluate side-chains 124 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 499 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6620 Z= 0.225 Angle : 0.664 8.551 8964 Z= 0.327 Chirality : 0.044 0.187 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.946 33.124 934 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.03 (0.29), residues: 856 helix: 1.13 (0.28), residues: 364 sheet: -2.22 (0.39), residues: 132 loop : -1.99 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 768 HIS 0.005 0.001 HIS A 733 PHE 0.013 0.001 PHE B 760 TYR 0.009 0.001 TYR B 573 ARG 0.005 0.000 ARG B 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.7578 (mpp) cc_final: 0.7219 (mpp) REVERT: A 362 MET cc_start: 0.8354 (ptp) cc_final: 0.8022 (tpp) REVERT: A 365 LEU cc_start: 0.8423 (mt) cc_final: 0.8133 (mt) REVERT: A 503 MET cc_start: 0.8278 (tpp) cc_final: 0.8019 (tmm) REVERT: A 516 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6297 (pt0) REVERT: A 601 MET cc_start: 0.8127 (tmm) cc_final: 0.7870 (tmm) REVERT: A 611 MET cc_start: 0.7981 (tpp) cc_final: 0.7740 (ttp) REVERT: A 672 ASN cc_start: 0.8833 (m110) cc_final: 0.8605 (m110) REVERT: A 690 ASP cc_start: 0.7859 (p0) cc_final: 0.7633 (p0) REVERT: B 351 MET cc_start: 0.7684 (mpp) cc_final: 0.7335 (mpp) REVERT: B 388 ILE cc_start: 0.9127 (pt) cc_final: 0.8899 (pt) REVERT: B 504 GLU cc_start: 0.8576 (pp20) cc_final: 0.8074 (pp20) REVERT: B 505 LEU cc_start: 0.7535 (mt) cc_final: 0.7135 (mp) REVERT: B 672 ASN cc_start: 0.8837 (m110) cc_final: 0.8621 (m110) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1706 time to fit residues: 34.3446 Evaluate side-chains 122 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102840 restraints weight = 11957.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106668 restraints weight = 7559.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109440 restraints weight = 5520.554| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6620 Z= 0.179 Angle : 0.652 8.501 8964 Z= 0.318 Chirality : 0.043 0.185 1048 Planarity : 0.004 0.036 1174 Dihedral : 4.836 32.502 934 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.93 (0.30), residues: 856 helix: 1.13 (0.28), residues: 364 sheet: -2.08 (0.40), residues: 132 loop : -1.88 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 768 HIS 0.005 0.001 HIS A 733 PHE 0.009 0.001 PHE B 760 TYR 0.008 0.001 TYR A 654 ARG 0.004 0.000 ARG B 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.05 seconds wall clock time: 32 minutes 24.61 seconds (1944.61 seconds total)