Starting phenix.real_space_refine (version: dev) on Sun Dec 11 17:35:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/12_2022/3j9d_6239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/12_2022/3j9d_6239.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/3j9d_6239/12_2022/3j9d_6239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/12_2022/3j9d_6239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/12_2022/3j9d_6239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/12_2022/3j9d_6239.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 0.220 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ASP 669": "OD1" <-> "OD2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 802": "NH1" <-> "NH2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 6086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6086 Unusual residues: {' ZN': 1} Classifications: {'peptide': 746, 'undetermined': 1} Link IDs: {'CIS': 14, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 701, None: 1} Not linked: pdbres="VAL A 961 " pdbres=" ZN A1001 " Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1310 SG CYS A 162 20.064 54.313 30.963 1.00 92.09 S ATOM 3290 SG CYS A 617 23.647 56.157 31.648 1.00 70.99 S ATOM 5217 SG CYS A 851 20.362 53.869 34.614 1.00 39.61 S Time building chain proxies: 3.97, per 1000 atoms: 0.65 Number of scatterers: 6086 At special positions: 0 Unit cell: (84.84, 107.06, 81.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 32 16.00 O 1105 8.00 N 1057 7.00 C 3891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 963.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 164 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 162 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 617 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 851 " Number of angles added : 3 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 35.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 144 through 148 removed outlier: 4.027A pdb=" N THR A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.544A pdb=" N ASP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.506A pdb=" N ILE A 487 " --> pdb=" O MET A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.917A pdb=" N ARG A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 638 removed outlier: 3.598A pdb=" N THR A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 669 through 682 WARNING: missing atoms! Processing helix chain 'A' and resid 690 through 704 removed outlier: 3.817A pdb=" N MET A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.851A pdb=" N LEU A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 732 through 737 removed outlier: 3.998A pdb=" N ILE A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 741 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.454A pdb=" N PHE A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.407A pdb=" N GLU A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 798 through 804 Processing helix chain 'A' and resid 808 through 822 removed outlier: 4.476A pdb=" N LYS A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 953 through 960 Processing sheet with id= A, first strand: chain 'A' and resid 130 through 133 removed outlier: 10.664A pdb=" N PHE A 23 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 25 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 4 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 938 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.864A pdb=" N ARG A 37 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 70 through 71 Processing sheet with id= D, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= E, first strand: chain 'A' and resid 149 through 150 removed outlier: 6.508A pdb=" N ILE A 871 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 903 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= G, first strand: chain 'A' and resid 409 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 760 through 765 197 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 6038 1.54 - 1.90: 179 1.90 - 2.25: 3 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 6221 Sorted by residual: bond pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 1.791 2.960 -1.169 2.50e-02 1.60e+03 2.19e+03 bond pdb=" CD2 TYR A 465 " pdb=" CE2 TYR A 465 " ideal model delta sigma weight residual 1.382 2.067 -0.685 3.00e-02 1.11e+03 5.21e+02 bond pdb=" CD1 TYR A 465 " pdb=" CE1 TYR A 465 " ideal model delta sigma weight residual 1.382 2.059 -0.677 3.00e-02 1.11e+03 5.10e+02 bond pdb=" CE1 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.812 -0.434 2.40e-02 1.74e+03 3.27e+02 bond pdb=" CE2 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.801 -0.423 2.40e-02 1.74e+03 3.11e+02 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 95.49 - 105.27: 151 105.27 - 115.06: 3692 115.06 - 124.84: 4446 124.84 - 134.63: 128 134.63 - 144.42: 3 Bond angle restraints: 8420 Sorted by residual: angle pdb=" N HIS A 16 " pdb=" CA HIS A 16 " pdb=" C HIS A 16 " ideal model delta sigma weight residual 111.11 95.49 15.62 1.20e+00 6.94e-01 1.70e+02 angle pdb=" CG MET A 771 " pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 100.90 129.48 -28.58 2.20e+00 2.07e-01 1.69e+02 angle pdb=" C HIS A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 104.48 15.36 1.25e+00 6.40e-01 1.51e+02 angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 112.29 122.07 -9.78 9.40e-01 1.13e+00 1.08e+02 angle pdb=" N GLU A 715 " pdb=" CA GLU A 715 " pdb=" C GLU A 715 " ideal model delta sigma weight residual 113.18 99.89 13.29 1.33e+00 5.65e-01 9.99e+01 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3047 17.68 - 35.36: 463 35.36 - 53.04: 191 53.04 - 70.72: 47 70.72 - 88.40: 8 Dihedral angle restraints: 3756 sinusoidal: 1560 harmonic: 2196 Sorted by residual: dihedral pdb=" CA VAL A 27 " pdb=" C VAL A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta harmonic sigma weight residual 0.00 38.21 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA HIS A 38 " pdb=" C HIS A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 55 " pdb=" C SER A 55 " pdb=" N ILE A 56 " pdb=" CA ILE A 56 " ideal model delta harmonic sigma weight residual -180.00 -148.27 -31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 749 0.101 - 0.203: 160 0.203 - 0.304: 17 0.304 - 0.405: 2 0.405 - 0.506: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 670 " pdb=" CA ILE A 670 " pdb=" CG1 ILE A 670 " pdb=" CG2 ILE A 670 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 926 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 618 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C PRO A 618 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO A 618 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 619 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 653 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 654 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 16 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C HIS A 16 " -0.058 2.00e-02 2.50e+03 pdb=" O HIS A 16 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 17 " 0.019 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 158 2.61 - 3.18: 5710 3.18 - 3.75: 9704 3.75 - 4.33: 13753 4.33 - 4.90: 21601 Nonbonded interactions: 50926 Sorted by model distance: nonbonded pdb=" O ASN A 47 " pdb=" ND2 ASN A 47 " model vdw 2.034 2.520 nonbonded pdb=" O PHE A 803 " pdb=" N LYS A 805 " model vdw 2.131 2.520 nonbonded pdb=" NE ARG A 74 " pdb=" OD2 ASP A 114 " model vdw 2.162 2.520 nonbonded pdb=" N GLU A 184 " pdb=" OE1 GLU A 184 " model vdw 2.234 2.520 nonbonded pdb=" OG1 THR A 506 " pdb=" N THR A 507 " model vdw 2.247 2.520 ... (remaining 50921 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 32 5.16 5 C 3891 2.51 5 N 1057 2.21 5 O 1105 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.140 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: 1.350 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.050 Process input model: 20.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 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 : 0.027 1.169 6221 Z= 1.945 Angle : 2.041 28.578 8420 Z= 1.287 Chirality : 0.083 0.506 929 Planarity : 0.009 0.086 1078 Dihedral : 20.567 88.397 2342 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 2.16 % Allowed : 8.22 % Favored : 89.62 % Rotamer Outliers : 24.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.82 % Twisted Proline : 0.00 % Twisted General : 0.84 % 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: -3.64 (0.29), residues: 742 helix: -3.11 (0.25), residues: 222 sheet: -2.97 (0.37), residues: 153 loop : -1.54 (0.34), residues: 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 144 time to evaluate : 0.835 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 166 outliers final: 72 residues processed: 273 average time/residue: 0.2253 time to fit residues: 76.6148 Evaluate side-chains 184 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 112 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.0850 time to fit residues: 10.7614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN A 947 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.166 6221 Z= 1.641 Angle : 0.929 28.907 8420 Z= 0.459 Chirality : 0.048 0.157 929 Planarity : 0.005 0.047 1078 Dihedral : 7.441 33.951 833 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.55 % Favored : 91.78 % Rotamer Outliers : 4.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.67 (0.28), residues: 742 helix: -1.52 (0.30), residues: 221 sheet: -2.07 (0.40), residues: 134 loop : -1.76 (0.30), residues: 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 0.747 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 13 residues processed: 167 average time/residue: 0.1837 time to fit residues: 40.2049 Evaluate side-chains 123 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0610 time to fit residues: 2.4218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.164 6221 Z= 1.639 Angle : 0.844 28.916 8420 Z= 0.416 Chirality : 0.047 0.164 929 Planarity : 0.004 0.045 1078 Dihedral : 6.618 35.125 833 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.36 % Favored : 90.97 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.40 (0.28), residues: 742 helix: -0.97 (0.32), residues: 226 sheet: -1.96 (0.38), residues: 134 loop : -1.80 (0.30), residues: 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.837 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 10 residues processed: 138 average time/residue: 0.1918 time to fit residues: 34.6767 Evaluate side-chains 120 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0627 time to fit residues: 2.1948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 474 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.637 Angle : 0.811 28.516 8420 Z= 0.398 Chirality : 0.046 0.154 929 Planarity : 0.004 0.033 1078 Dihedral : 6.238 35.420 833 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.36 % Favored : 90.97 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.21 (0.28), residues: 742 helix: -0.57 (0.33), residues: 229 sheet: -1.78 (0.39), residues: 134 loop : -1.89 (0.30), residues: 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.759 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 12 residues processed: 148 average time/residue: 0.1801 time to fit residues: 35.1503 Evaluate side-chains 118 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0612 time to fit residues: 2.2892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.636 Angle : 0.796 28.476 8420 Z= 0.389 Chirality : 0.045 0.168 929 Planarity : 0.004 0.034 1078 Dihedral : 6.011 34.676 833 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.95 % Favored : 91.37 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.20 (0.29), residues: 742 helix: -0.36 (0.34), residues: 230 sheet: -2.18 (0.41), residues: 124 loop : -1.89 (0.29), residues: 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.784 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 13 residues processed: 133 average time/residue: 0.1720 time to fit residues: 30.4316 Evaluate side-chains 121 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0570 time to fit residues: 2.3596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.637 Angle : 0.790 28.471 8420 Z= 0.387 Chirality : 0.045 0.170 929 Planarity : 0.004 0.039 1078 Dihedral : 5.925 33.911 833 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.76 % Favored : 90.70 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.02 (0.29), residues: 742 helix: -0.26 (0.34), residues: 230 sheet: -1.88 (0.42), residues: 124 loop : -1.82 (0.29), residues: 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.784 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 5 residues processed: 126 average time/residue: 0.1727 time to fit residues: 29.3893 Evaluate side-chains 110 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0703 time to fit residues: 1.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.145 6221 Z= 1.644 Angle : 0.816 29.081 8420 Z= 0.402 Chirality : 0.047 0.171 929 Planarity : 0.004 0.040 1078 Dihedral : 6.036 34.465 833 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.89 % Favored : 90.43 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.00 (0.29), residues: 742 helix: -0.40 (0.34), residues: 231 sheet: -1.78 (0.44), residues: 124 loop : -1.74 (0.30), residues: 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.763 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.1832 time to fit residues: 27.3934 Evaluate side-chains 111 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0630 time to fit residues: 1.8150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.158 6221 Z= 1.639 Angle : 0.797 28.861 8420 Z= 0.392 Chirality : 0.046 0.184 929 Planarity : 0.004 0.041 1078 Dihedral : 5.948 34.676 833 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.95 % Favored : 91.37 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.95 (0.30), residues: 742 helix: -0.31 (0.34), residues: 231 sheet: -1.71 (0.44), residues: 124 loop : -1.75 (0.30), residues: 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.788 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 0.1862 time to fit residues: 29.0115 Evaluate side-chains 110 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0617 time to fit residues: 1.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.159 6221 Z= 1.662 Angle : 0.847 28.499 8420 Z= 0.419 Chirality : 0.048 0.169 929 Planarity : 0.005 0.040 1078 Dihedral : 6.183 34.823 833 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.57 % Favored : 89.76 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.06 (0.29), residues: 742 helix: -0.60 (0.33), residues: 234 sheet: -1.64 (0.44), residues: 124 loop : -1.74 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.792 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.1993 time to fit residues: 28.7790 Evaluate side-chains 103 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0642 time to fit residues: 1.7418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.159 6221 Z= 1.638 Angle : 0.796 28.494 8420 Z= 0.393 Chirality : 0.046 0.187 929 Planarity : 0.004 0.040 1078 Dihedral : 5.922 35.094 833 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.49 % Favored : 90.84 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.78 (0.30), residues: 742 helix: -0.23 (0.34), residues: 231 sheet: -0.98 (0.47), residues: 112 loop : -1.84 (0.29), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.789 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 0.1833 time to fit residues: 27.7956 Evaluate side-chains 102 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2005 time to fit residues: 1.5156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 0.0040 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093988 restraints weight = 8555.618| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.75 r_work: 0.2863 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 1.159 6221 Z= 1.637 Angle : 0.787 28.481 8420 Z= 0.387 Chirality : 0.045 0.184 929 Planarity : 0.004 0.041 1078 Dihedral : 5.796 33.661 833 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.49 % Favored : 90.84 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.64 (0.30), residues: 742 helix: -0.12 (0.35), residues: 232 sheet: -0.78 (0.49), residues: 112 loop : -1.81 (0.30), residues: 398 =============================================================================== Job complete usr+sys time: 1638.72 seconds wall clock time: 30 minutes 13.04 seconds (1813.04 seconds total)