Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 20:42:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/08_2023/8dvr_27743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/08_2023/8dvr_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_27743/08_2023/8dvr_27743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/08_2023/8dvr_27743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/08_2023/8dvr_27743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvr_27743/08_2023/8dvr_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-1.21rc1-5044/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: 3.72, per 1000 atoms: 0.66 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: 2.56 Conformation dependent library (CDL) restraints added in 902.9 milliseconds 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: 2.28 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: 1.98 Time building geometry restraints manager: 2.56 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: 3130 17.86 - 35.71: 262 35.71 - 53.57: 53 53.57 - 71.43: 7 71.43 - 89.28: 9 Dihedral angle restraints: 3461 sinusoidal: 1589 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 3458 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: 0.460 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: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- 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 : 13.618 89.284 2241 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 % 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 *********************** 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 : 0.659 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.2312 time to fit residues: 39.3796 Evaluate side-chains 92 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0551 time to fit residues: 1.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5758 Z= 0.175 Angle : 0.482 8.206 7872 Z= 0.234 Chirality : 0.038 0.183 893 Planarity : 0.003 0.036 924 Dihedral : 5.902 89.341 935 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 2.98 % 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: -1.20 (0.33), residues: 627 helix: 1.29 (0.30), residues: 283 sheet: -2.98 (0.56), residues: 78 loop : -2.49 (0.34), residues: 266 *********************** 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 108 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.638 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 0.1866 time to fit residues: 24.5421 Evaluate side-chains 81 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0538 time to fit residues: 1.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7586 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5758 Z= 0.151 Angle : 0.479 8.126 7872 Z= 0.229 Chirality : 0.039 0.186 893 Planarity : 0.003 0.041 924 Dihedral : 6.093 91.711 935 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.34), residues: 627 helix: 1.70 (0.31), residues: 283 sheet: -2.95 (0.53), residues: 84 loop : -2.35 (0.35), residues: 260 *********************** 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 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 92 average time/residue: 0.1923 time to fit residues: 23.1733 Evaluate side-chains 74 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0569 time to fit residues: 1.0836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5758 Z= 0.172 Angle : 0.502 8.348 7872 Z= 0.240 Chirality : 0.039 0.167 893 Planarity : 0.003 0.034 924 Dihedral : 6.272 94.392 935 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 2.45 % 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: -0.59 (0.34), residues: 627 helix: 2.00 (0.31), residues: 276 sheet: -2.85 (0.53), residues: 84 loop : -2.23 (0.35), residues: 267 *********************** 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 94 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.649 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.2074 time to fit residues: 23.3468 Evaluate side-chains 82 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0540 time to fit residues: 1.5143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5758 Z= 0.173 Angle : 0.508 10.532 7872 Z= 0.241 Chirality : 0.039 0.164 893 Planarity : 0.003 0.033 924 Dihedral : 6.354 94.944 935 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.35), residues: 627 helix: 2.04 (0.31), residues: 285 sheet: -2.75 (0.52), residues: 84 loop : -2.14 (0.36), residues: 258 *********************** 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 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.630 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1886 time to fit residues: 19.6028 Evaluate side-chains 68 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0552 time to fit residues: 1.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.0670 chunk 52 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 A 786 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2833 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= 0.120 Angle : 0.472 9.227 7872 Z= 0.224 Chirality : 0.038 0.133 893 Planarity : 0.003 0.033 924 Dihedral : 6.210 92.482 935 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 1.23 % 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: -0.10 (0.35), residues: 627 helix: 2.24 (0.31), residues: 285 sheet: -2.30 (0.56), residues: 78 loop : -2.06 (0.36), residues: 264 *********************** 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 83 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.639 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.1740 time to fit residues: 18.5448 Evaluate side-chains 72 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0593 time to fit residues: 1.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7736 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 5758 Z= 0.268 Angle : 0.606 9.657 7872 Z= 0.292 Chirality : 0.042 0.240 893 Planarity : 0.003 0.032 924 Dihedral : 6.644 96.656 935 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.70 % 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: -0.22 (0.34), residues: 627 helix: 2.03 (0.30), residues: 286 sheet: -2.25 (0.53), residues: 84 loop : -2.01 (0.36), residues: 257 *********************** 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 76 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.613 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.1825 time to fit residues: 18.1830 Evaluate side-chains 66 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0560 time to fit residues: 1.0777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3274 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= 0.170 Angle : 0.549 8.720 7872 Z= 0.263 Chirality : 0.041 0.240 893 Planarity : 0.003 0.043 924 Dihedral : 6.502 96.349 935 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.23 % 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: 0.01 (0.35), residues: 627 helix: 2.18 (0.31), residues: 289 sheet: -2.09 (0.56), residues: 78 loop : -1.91 (0.36), residues: 260 *********************** 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 74 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.654 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1891 time to fit residues: 17.9397 Evaluate side-chains 67 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0603 time to fit residues: 1.3731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 5758 Z= 0.257 Angle : 0.597 9.515 7872 Z= 0.286 Chirality : 0.042 0.236 893 Planarity : 0.004 0.044 924 Dihedral : 6.785 97.686 935 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.18 % 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: 1.95 (0.30), residues: 293 sheet: -2.06 (0.57), residues: 79 loop : -1.81 (0.37), residues: 255 *********************** 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 66 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.655 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.2202 time to fit residues: 18.4138 Evaluate side-chains 63 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0554 time to fit residues: 0.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5758 Z= 0.186 Angle : 0.557 8.612 7872 Z= 0.267 Chirality : 0.041 0.230 893 Planarity : 0.003 0.045 924 Dihedral : 6.629 97.524 935 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.00 % 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: 0.08 (0.35), residues: 627 helix: 2.13 (0.31), residues: 289 sheet: -1.92 (0.58), residues: 78 loop : -1.79 (0.37), residues: 260 ********************** 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 67 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.667 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2125 time to fit residues: 18.4147 Evaluate side-chains 65 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124005 restraints weight = 6400.281| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.93 r_work: 0.3190 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3499 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= 0.183 Angle : 0.547 8.716 7872 Z= 0.262 Chirality : 0.041 0.228 893 Planarity : 0.003 0.044 924 Dihedral : 6.571 97.123 935 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.18 % 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: 2.17 (0.31), residues: 290 sheet: -2.05 (0.55), residues: 85 loop : -1.68 (0.38), residues: 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.89 seconds wall clock time: 27 minutes 32.79 seconds (1652.79 seconds total)