Starting phenix.real_space_refine on Tue Feb 13 11:02:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/02_2024/8dvr_27743_updated.pdb" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ASP 919": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 445 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 23.312 29.188 27.887 1.00 29.78 S ATOM 4630 SG CYS A 864 19.045 29.309 28.690 1.00 26.94 S ATOM 4669 SG CYS A 869 21.454 27.047 30.233 1.00 32.07 S Time building chain proxies: 3.84, per 1000 atoms: 0.69 Number of scatterers: 5601 At special positions: 0 Unit cell: (79.032, 99.324, 85.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 24 15.00 O 1106 8.00 N 947 7.00 C 3492 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 5 sheets defined 44.4% alpha, 8.5% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.515A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 434 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.331A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.794A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.596A pdb=" N ASP A 641 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 Processing helix chain 'A' and resid 773 through 793 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.990A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 836 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 293 through 296 removed outlier: 6.173A pdb=" N LEU A 368 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE A 296 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 370 " --> pdb=" O PHE A 296 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 458 through 462 removed outlier: 7.056A pdb=" N CYS A 738 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG A 461 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 740 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.698A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.940A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.58 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: 1711 1.34 - 1.46: 902 1.46 - 1.57: 3057 1.57 - 1.69: 45 1.69 - 1.81: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C ILE A 884 " pdb=" O ILE A 884 " ideal model delta sigma weight residual 1.232 1.241 -0.009 8.90e-03 1.26e+04 9.64e-01 bond pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.60e-01 bond pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.38e-01 bond pdb=" C VAL A 414 " pdb=" N GLY A 415 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.79e-01 bond pdb=" CA ILE A 916 " pdb=" CB ILE A 916 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 4.96e-01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.48: 293 107.48 - 114.10: 3350 114.10 - 120.72: 2343 120.72 - 127.34: 1800 127.34 - 133.96: 86 Bond angle restraints: 7872 Sorted by residual: angle pdb=" N ILE A 897 " pdb=" CA ILE A 897 " pdb=" C ILE A 897 " ideal model delta sigma weight residual 111.90 109.07 2.83 8.10e-01 1.52e+00 1.22e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.90 109.36 2.54 8.10e-01 1.52e+00 9.82e+00 angle pdb=" N ALA A 410 " pdb=" CA ALA A 410 " pdb=" C ALA A 410 " ideal model delta sigma weight residual 114.04 110.54 3.50 1.24e+00 6.50e-01 7.98e+00 angle pdb=" C2' GTP B 201 " pdb=" C3' GTP B 201 " pdb=" C4' GTP B 201 " ideal model delta sigma weight residual 111.00 103.89 7.11 3.00e+00 1.11e-01 5.62e+00 angle pdb=" N ILE A 884 " pdb=" CA ILE A 884 " pdb=" C ILE A 884 " ideal model delta sigma weight residual 107.61 110.31 -2.70 1.19e+00 7.06e-01 5.14e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3153 17.86 - 35.71: 265 35.71 - 53.57: 73 53.57 - 71.43: 29 71.43 - 89.28: 15 Dihedral angle restraints: 3535 sinusoidal: 1663 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 23.63 80.96 1 2.00e+01 2.50e-03 2.02e+01 dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU A 895 " pdb=" CG GLU A 895 " pdb=" CD GLU A 895 " pdb=" OE1 GLU A 895 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 557 0.024 - 0.049: 201 0.049 - 0.073: 75 0.073 - 0.098: 43 0.098 - 0.122: 17 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A 629 " pdb=" N ILE A 629 " pdb=" C ILE A 629 " pdb=" CB ILE A 629 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO A 382 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 300 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.26e-01 pdb=" N PRO A 301 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 884 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.12e-01 pdb=" N PRO A 885 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 885 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 885 " 0.011 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1369 2.79 - 3.32: 5240 3.32 - 3.85: 9463 3.85 - 4.37: 10771 4.37 - 4.90: 18068 Nonbonded interactions: 44911 Sorted by model distance: nonbonded pdb=" ND2 ASN A 259 " pdb=" O ASP A 435 " model vdw 2.267 2.520 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.325 2.440 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.342 2.440 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.349 2.440 nonbonded pdb=" N ASP A 580 " pdb=" OD1 ASP A 580 " model vdw 2.355 2.520 ... (remaining 44906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.900 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.740 Find NCS groups from input model: 0.130 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.002 0.020 5758 Z= 0.106 Angle : 0.456 7.111 7872 Z= 0.269 Chirality : 0.035 0.122 893 Planarity : 0.002 0.024 924 Dihedral : 15.720 89.284 2315 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.40 % Allowed : 9.46 % Favored : 89.14 % 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: -2.25 (0.31), residues: 627 helix: 0.37 (0.28), residues: 280 sheet: -3.31 (0.51), residues: 81 loop : -3.00 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 847 PHE 0.007 0.001 PHE A 856 TYR 0.003 0.000 TYR A 390 ARG 0.001 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 492 ASP cc_start: 0.7105 (p0) cc_final: 0.6518 (t0) REVERT: A 759 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7442 (ttpp) REVERT: A 763 ASP cc_start: 0.7733 (t70) cc_final: 0.7508 (t0) REVERT: A 789 PHE cc_start: 0.7957 (t80) cc_final: 0.7567 (t80) REVERT: A 889 ILE cc_start: 0.9123 (tp) cc_final: 0.8588 (tp) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.2397 time to fit residues: 40.8854 Evaluate side-chains 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 380 GLN A 495 ASN A 517 GLN A 573 ASN A 876 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5758 Z= 0.149 Angle : 0.462 8.069 7872 Z= 0.222 Chirality : 0.038 0.174 893 Planarity : 0.003 0.037 924 Dihedral : 13.163 88.391 1015 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.98 % Allowed : 11.91 % Favored : 85.11 % 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: -1.17 (0.33), residues: 627 helix: 1.34 (0.31), residues: 282 sheet: -2.95 (0.56), residues: 78 loop : -2.49 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.002 0.000 HIS A 871 PHE 0.007 0.001 PHE A 913 TYR 0.009 0.001 TYR A 383 ARG 0.007 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.621 Fit side-chains REVERT: A 255 MET cc_start: 0.8485 (mtt) cc_final: 0.7959 (mtt) REVERT: A 492 ASP cc_start: 0.7195 (p0) cc_final: 0.6594 (t0) REVERT: A 632 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 647 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 653 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7892 (pp) REVERT: A 759 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7510 (ttpp) REVERT: A 763 ASP cc_start: 0.7840 (t70) cc_final: 0.7552 (t0) REVERT: A 789 PHE cc_start: 0.7957 (t80) cc_final: 0.7657 (t80) REVERT: A 872 ASP cc_start: 0.7890 (t0) cc_final: 0.7449 (t0) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.1887 time to fit residues: 24.7965 Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5758 Z= 0.169 Angle : 0.486 8.299 7872 Z= 0.235 Chirality : 0.039 0.178 893 Planarity : 0.003 0.038 924 Dihedral : 13.180 93.733 1011 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.85 % Allowed : 13.84 % Favored : 82.31 % 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 (0.34), residues: 627 helix: 1.72 (0.31), residues: 281 sheet: -2.95 (0.53), residues: 84 loop : -2.36 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.002 0.001 HIS A 281 PHE 0.012 0.001 PHE A 616 TYR 0.009 0.001 TYR A 383 ARG 0.008 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.681 Fit side-chains REVERT: A 461 ARG cc_start: 0.6993 (mtp85) cc_final: 0.6646 (mtp85) REVERT: A 492 ASP cc_start: 0.7359 (p0) cc_final: 0.6709 (t0) REVERT: A 632 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 653 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7947 (pp) REVERT: A 693 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 755 MET cc_start: 0.6230 (mtm) cc_final: 0.6013 (mtm) REVERT: A 759 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7569 (ttpp) REVERT: A 763 ASP cc_start: 0.7851 (t70) cc_final: 0.7599 (t0) REVERT: A 872 ASP cc_start: 0.8073 (t0) cc_final: 0.7851 (t0) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 0.1790 time to fit residues: 22.5784 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5758 Z= 0.233 Angle : 0.538 8.864 7872 Z= 0.260 Chirality : 0.040 0.179 893 Planarity : 0.003 0.037 924 Dihedral : 13.222 95.669 1011 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.80 % Allowed : 17.69 % Favored : 79.51 % 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: -0.64 (0.34), residues: 627 helix: 1.78 (0.31), residues: 283 sheet: -2.64 (0.54), residues: 79 loop : -2.25 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.003 0.001 HIS A 871 PHE 0.009 0.001 PHE A 590 TYR 0.011 0.001 TYR A 383 ARG 0.010 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.666 Fit side-chains REVERT: A 461 ARG cc_start: 0.7019 (mtp85) cc_final: 0.6768 (mtp180) REVERT: A 632 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8331 (tt) REVERT: A 653 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (pp) REVERT: A 759 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7514 (ttpp) REVERT: A 763 ASP cc_start: 0.7884 (t70) cc_final: 0.7625 (t0) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.1881 time to fit residues: 21.9219 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5758 Z= 0.143 Angle : 0.482 8.039 7872 Z= 0.233 Chirality : 0.039 0.160 893 Planarity : 0.003 0.033 924 Dihedral : 13.223 94.675 1011 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.80 % Allowed : 19.61 % Favored : 77.58 % 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: -0.42 (0.35), residues: 627 helix: 2.11 (0.31), residues: 281 sheet: -2.72 (0.52), residues: 84 loop : -2.18 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 646 HIS 0.005 0.001 HIS A 786 PHE 0.016 0.001 PHE A 460 TYR 0.008 0.001 TYR A 390 ARG 0.004 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.6928 (mtp85) cc_final: 0.6569 (mtp85) REVERT: A 632 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8336 (tt) REVERT: A 653 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7924 (pp) REVERT: A 759 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7502 (ttpp) REVERT: A 763 ASP cc_start: 0.7848 (t70) cc_final: 0.7637 (t0) REVERT: A 794 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6738 (pp30) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.1839 time to fit residues: 21.2880 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.0670 chunk 52 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5758 Z= 0.119 Angle : 0.460 7.776 7872 Z= 0.222 Chirality : 0.038 0.140 893 Planarity : 0.003 0.033 924 Dihedral : 13.157 92.094 1011 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.33 % Allowed : 19.61 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.35), residues: 627 helix: 2.26 (0.31), residues: 286 sheet: -2.42 (0.51), residues: 88 loop : -2.08 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.007 0.001 HIS A 786 PHE 0.016 0.001 PHE A 460 TYR 0.009 0.001 TYR A 390 ARG 0.004 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.603 Fit side-chains REVERT: A 632 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 653 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7892 (pp) REVERT: A 759 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7547 (ttpp) REVERT: A 794 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6703 (pp30) outliers start: 19 outliers final: 10 residues processed: 87 average time/residue: 0.1789 time to fit residues: 20.5457 Evaluate side-chains 80 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5758 Z= 0.173 Angle : 0.502 8.565 7872 Z= 0.242 Chirality : 0.039 0.232 893 Planarity : 0.003 0.040 924 Dihedral : 13.167 94.739 1011 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.15 % Allowed : 20.14 % Favored : 76.71 % 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: -0.09 (0.35), residues: 627 helix: 2.23 (0.31), residues: 288 sheet: -2.25 (0.56), residues: 82 loop : -2.09 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 873 HIS 0.005 0.001 HIS A 786 PHE 0.015 0.001 PHE A 460 TYR 0.009 0.001 TYR A 390 ARG 0.005 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.627 Fit side-chains REVERT: A 526 PRO cc_start: 0.8193 (Cg_endo) cc_final: 0.7850 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 653 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7936 (pp) REVERT: A 759 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7595 (ttpp) REVERT: A 794 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6708 (pp30) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.1785 time to fit residues: 20.3394 Evaluate side-chains 82 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5758 Z= 0.182 Angle : 0.527 8.719 7872 Z= 0.254 Chirality : 0.040 0.229 893 Planarity : 0.003 0.038 924 Dihedral : 13.210 95.449 1011 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.15 % Allowed : 21.19 % Favored : 75.66 % 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: -0.05 (0.35), residues: 627 helix: 2.24 (0.31), residues: 286 sheet: -2.12 (0.55), residues: 88 loop : -2.03 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 873 HIS 0.008 0.001 HIS A 786 PHE 0.016 0.001 PHE A 460 TYR 0.009 0.001 TYR A 390 ARG 0.006 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.651 Fit side-chains REVERT: A 526 PRO cc_start: 0.8211 (Cg_endo) cc_final: 0.7872 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 653 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (pp) REVERT: A 759 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7655 (ttpp) REVERT: A 794 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6623 (pp30) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1988 time to fit residues: 22.2467 Evaluate side-chains 85 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5758 Z= 0.211 Angle : 0.547 9.246 7872 Z= 0.263 Chirality : 0.041 0.221 893 Planarity : 0.003 0.037 924 Dihedral : 13.257 96.024 1011 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.33 % Allowed : 20.84 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.35), residues: 627 helix: 2.23 (0.31), residues: 284 sheet: -2.07 (0.58), residues: 82 loop : -2.02 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 873 HIS 0.002 0.001 HIS A 281 PHE 0.018 0.001 PHE A 460 TYR 0.010 0.001 TYR A 390 ARG 0.007 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 526 PRO cc_start: 0.8198 (Cg_endo) cc_final: 0.7863 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 759 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7662 (ttpp) REVERT: A 794 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6626 (pp30) outliers start: 19 outliers final: 14 residues processed: 86 average time/residue: 0.2023 time to fit residues: 22.4743 Evaluate side-chains 83 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 15 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.002 0.029 5758 Z= 0.143 Angle : 0.510 8.291 7872 Z= 0.246 Chirality : 0.040 0.216 893 Planarity : 0.003 0.038 924 Dihedral : 13.226 94.469 1011 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.80 % Allowed : 21.19 % Favored : 76.01 % 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: 0.12 (0.35), residues: 627 helix: 2.48 (0.31), residues: 282 sheet: -2.18 (0.55), residues: 90 loop : -1.92 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 512 HIS 0.001 0.000 HIS A 830 PHE 0.019 0.001 PHE A 616 TYR 0.010 0.001 TYR A 390 ARG 0.005 0.000 ARG A 811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 526 PRO cc_start: 0.8189 (Cg_endo) cc_final: 0.7855 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8389 (tt) REVERT: A 653 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7945 (pp) REVERT: A 759 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7637 (ttpp) REVERT: A 794 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6779 (pp30) REVERT: A 878 LYS cc_start: 0.7096 (ptmm) cc_final: 0.6873 (ptmm) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.2100 time to fit residues: 21.1524 Evaluate side-chains 79 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121403 restraints weight = 6429.539| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.96 r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5758 Z= 0.220 Angle : 0.551 9.386 7872 Z= 0.264 Chirality : 0.041 0.220 893 Planarity : 0.003 0.039 924 Dihedral : 13.249 96.139 1011 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.80 % Allowed : 21.37 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.35), residues: 627 helix: 2.24 (0.31), residues: 287 sheet: -2.20 (0.57), residues: 85 loop : -1.86 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 873 HIS 0.002 0.001 HIS A 876 PHE 0.019 0.001 PHE A 616 TYR 0.010 0.001 TYR A 390 ARG 0.008 0.000 ARG A 811 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.66 seconds wall clock time: 28 minutes 21.09 seconds (1701.09 seconds total)