Starting phenix.real_space_refine on Thu Feb 15 12:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2l_27142/02_2024/8d2l_27142_updated.pdb" } resolution = 2.21 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= 0.006 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 P 151 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6892 2.51 5 N 2199 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 847": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12227 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2080 Unusual residues: {'GTP': 1} Classifications: {'RNA': 96, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 44, 'rna3p_pyr': 40} Link IDs: {'rna2p': 12, 'rna3p': 83, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 12} Chain: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.82, per 1000 atoms: 0.64 Number of scatterers: 12227 At special positions: 0 Unit cell: (95.7, 106.425, 129.525, 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) S 20 16.00 P 151 15.00 Mg 10 11.99 O 2955 8.00 N 2199 7.00 C 6892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.08 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.12 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 613 " distance=2.08 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.07 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: 6.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 7 sheets defined 43.3% alpha, 8.7% beta 56 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 60 through 91 Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 5.196A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 487 through 507 Processing helix chain 'A' and resid 525 through 551 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 682 through 702 Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'A' and resid 726 through 729 No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 747 through 759 Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 810 through 819 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 957 through 962 Processing helix chain 'A' and resid 982 through 985 No H-bonds generated for 'chain 'A' and resid 982 through 985' Processing helix chain 'A' and resid 989 through 996 Processing helix chain 'A' and resid 1025 through 1032 removed outlier: 3.962A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1069 removed outlier: 4.146A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1085 Processing helix chain 'A' and resid 1094 through 1097 No H-bonds generated for 'chain 'A' and resid 1094 through 1097' Processing sheet with id= A, first strand: chain 'A' and resid 706 through 711 removed outlier: 3.829A pdb=" N SER A 512 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 19 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 30 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE A 39 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= C, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= D, first strand: chain 'A' and resid 846 through 849 Processing sheet with id= E, first strand: chain 'A' and resid 921 through 924 Processing sheet with id= F, first strand: chain 'A' and resid 1104 through 1106 removed outlier: 3.772A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.653A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2464 1.33 - 1.46: 4671 1.46 - 1.60: 5094 1.60 - 1.73: 176 1.73 - 1.87: 28 Bond restraints: 12433 Sorted by residual: bond pdb=" C3' DC X 3 " pdb=" O3' DC X 3 " ideal model delta sigma weight residual 1.422 1.506 -0.084 3.00e-02 1.11e+03 7.78e+00 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.80e+00 bond pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta sigma weight residual 1.530 1.567 -0.037 1.69e-02 3.50e+03 4.68e+00 bond pdb=" CA ASP A 53 " pdb=" CB ASP A 53 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.69e-02 3.50e+03 4.32e+00 bond pdb=" O5' DA D 31 " pdb=" C5' DA D 31 " ideal model delta sigma weight residual 1.423 1.364 0.059 3.00e-02 1.11e+03 3.80e+00 ... (remaining 12428 not shown) Histogram of bond angle deviations from ideal: 93.96 - 103.58: 442 103.58 - 113.20: 7413 113.20 - 122.82: 8104 122.82 - 132.44: 1547 132.44 - 142.07: 50 Bond angle restraints: 17556 Sorted by residual: angle pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " pdb=" SG CYS A 613 " ideal model delta sigma weight residual 114.40 142.07 -27.67 2.30e+00 1.89e-01 1.45e+02 angle pdb=" N CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.16 100.24 9.92 1.48e+00 4.57e-01 4.49e+01 angle pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " pdb=" CG GLU A 33 " ideal model delta sigma weight residual 114.10 126.44 -12.34 2.00e+00 2.50e-01 3.81e+01 angle pdb=" N PRO A 892 " pdb=" CD PRO A 892 " pdb=" CG PRO A 892 " ideal model delta sigma weight residual 103.20 95.50 7.70 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.85 118.09 -7.24 1.70e+00 3.46e-01 1.81e+01 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6948 33.25 - 66.50: 521 66.50 - 99.75: 54 99.75 - 133.00: 3 133.00 - 166.25: 1 Dihedral angle restraints: 7527 sinusoidal: 4331 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -172.88 86.88 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CA ASP A 590 " pdb=" C ASP A 590 " pdb=" N HIS A 591 " pdb=" CA HIS A 591 " ideal model delta harmonic sigma weight residual 180.00 147.74 32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -141.31 55.31 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 7524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1725 0.066 - 0.132: 268 0.132 - 0.198: 19 0.198 - 0.264: 4 0.264 - 0.330: 4 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE A 24 " pdb=" CA ILE A 24 " pdb=" CG1 ILE A 24 " pdb=" CG2 ILE A 24 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2017 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.026 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 363 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1020 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A1020 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A1020 " 0.022 2.00e-02 2.50e+03 pdb=" N THR A1021 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 613 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C CYS A 613 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 613 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN A 614 " 0.019 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 327 2.60 - 3.18: 9730 3.18 - 3.75: 24232 3.75 - 4.33: 31917 4.33 - 4.90: 46821 Nonbonded interactions: 113027 Sorted by model distance: nonbonded pdb=" OE2 GLU A 516 " pdb="MG MG A1202 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.058 2.170 nonbonded pdb=" O3' DA X 13 " pdb="MG MG A1201 " model vdw 2.066 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 205 " model vdw 2.067 2.170 ... (remaining 113022 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=0.00 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 45.240 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 12433 Z= 0.302 Angle : 0.877 27.666 17556 Z= 0.466 Chirality : 0.049 0.330 2020 Planarity : 0.007 0.073 1738 Dihedral : 19.795 166.247 5435 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.15 (0.23), residues: 1097 helix: 0.34 (0.21), residues: 546 sheet: -0.27 (0.60), residues: 76 loop : -0.46 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 721 HIS 0.004 0.001 HIS A 574 PHE 0.071 0.003 PHE A 363 TYR 0.018 0.003 TYR A 986 ARG 0.011 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.115 Fit side-chains REVERT: A 21 GLU cc_start: 0.7780 (tp30) cc_final: 0.7527 (mm-30) REVERT: A 33 GLU cc_start: 0.6796 (pm20) cc_final: 0.6472 (pm20) REVERT: A 724 ILE cc_start: 0.7914 (mm) cc_final: 0.7690 (mp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 2.0373 time to fit residues: 251.6823 Evaluate side-chains 103 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 12433 Z= 0.340 Angle : 0.670 11.611 17556 Z= 0.349 Chirality : 0.042 0.220 2020 Planarity : 0.006 0.048 1738 Dihedral : 20.918 164.537 3346 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 6.56 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.58 (0.25), residues: 1097 helix: 1.00 (0.22), residues: 544 sheet: -0.08 (0.58), residues: 81 loop : -0.12 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 161 HIS 0.005 0.001 HIS A 138 PHE 0.027 0.003 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.005 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7065 (pm20) cc_final: 0.6800 (pp20) REVERT: A 230 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7604 (mpt-90) REVERT: A 261 GLU cc_start: 0.7958 (pm20) cc_final: 0.7678 (pm20) REVERT: A 724 ILE cc_start: 0.7945 (mm) cc_final: 0.7714 (mp) outliers start: 12 outliers final: 3 residues processed: 111 average time/residue: 2.0079 time to fit residues: 236.2142 Evaluate side-chains 102 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 12433 Z= 0.382 Angle : 0.702 11.693 17556 Z= 0.363 Chirality : 0.044 0.229 2020 Planarity : 0.006 0.042 1738 Dihedral : 20.959 161.146 3346 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.97 % Allowed : 7.54 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.68 (0.24), residues: 1097 helix: 1.07 (0.22), residues: 543 sheet: -0.07 (0.59), residues: 75 loop : -0.07 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.028 0.003 PHE A 282 TYR 0.022 0.003 TYR A 986 ARG 0.005 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7108 (pm20) cc_final: 0.6799 (pp20) REVERT: A 230 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7677 (mpt-90) REVERT: A 724 ILE cc_start: 0.7931 (mm) cc_final: 0.7701 (mp) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 1.9345 time to fit residues: 229.9000 Evaluate side-chains 109 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 12433 Z= 0.368 Angle : 0.681 10.874 17556 Z= 0.353 Chirality : 0.043 0.222 2020 Planarity : 0.006 0.041 1738 Dihedral : 20.912 161.011 3346 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.75 % Allowed : 8.85 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.78 (0.25), residues: 1097 helix: 1.18 (0.22), residues: 538 sheet: -0.05 (0.57), residues: 81 loop : -0.02 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.027 0.003 PHE A 282 TYR 0.022 0.003 TYR A 986 ARG 0.005 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7110 (pm20) cc_final: 0.6741 (pp20) REVERT: A 137 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.6405 (mtt180) REVERT: A 149 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8277 (ttmt) REVERT: A 230 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7671 (mpt-90) REVERT: A 372 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: A 679 GLN cc_start: 0.5511 (tt0) cc_final: 0.5179 (tt0) REVERT: A 724 ILE cc_start: 0.7944 (mm) cc_final: 0.7710 (mp) REVERT: A 891 LEU cc_start: 0.8000 (mt) cc_final: 0.7796 (mm) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 1.9792 time to fit residues: 238.1685 Evaluate side-chains 111 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 12433 Z= 0.198 Angle : 0.564 9.854 17556 Z= 0.295 Chirality : 0.037 0.214 2020 Planarity : 0.004 0.031 1738 Dihedral : 20.819 163.978 3346 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.98 % Allowed : 9.95 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.09 (0.25), residues: 1097 helix: 1.49 (0.22), residues: 538 sheet: -0.13 (0.59), residues: 76 loop : 0.10 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.019 0.002 PHE A 282 TYR 0.017 0.001 TYR A 986 ARG 0.002 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7096 (pm20) cc_final: 0.6792 (pp20) REVERT: A 137 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.6418 (mtt180) REVERT: A 230 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7651 (mpt-90) REVERT: A 724 ILE cc_start: 0.7959 (mm) cc_final: 0.7731 (mp) outliers start: 9 outliers final: 4 residues processed: 108 average time/residue: 2.0976 time to fit residues: 242.4294 Evaluate side-chains 108 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 12433 Z= 0.255 Angle : 0.594 9.709 17556 Z= 0.309 Chirality : 0.039 0.211 2020 Planarity : 0.005 0.030 1738 Dihedral : 20.827 163.916 3346 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.31 % Allowed : 10.16 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.14 (0.25), residues: 1097 helix: 1.54 (0.22), residues: 536 sheet: -0.03 (0.57), residues: 81 loop : 0.11 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.023 0.002 PHE A 282 TYR 0.019 0.002 TYR A 986 ARG 0.003 0.000 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7037 (pm20) cc_final: 0.6777 (pp20) REVERT: A 137 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.6419 (mtt180) REVERT: A 230 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7676 (mpt-90) REVERT: A 724 ILE cc_start: 0.7982 (mm) cc_final: 0.7744 (mp) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 1.8526 time to fit residues: 220.3532 Evaluate side-chains 115 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 100 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 12433 Z= 0.236 Angle : 0.581 10.868 17556 Z= 0.303 Chirality : 0.038 0.212 2020 Planarity : 0.004 0.030 1738 Dihedral : 20.816 164.320 3346 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.42 % Allowed : 10.27 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1097 helix: 1.60 (0.22), residues: 535 sheet: -0.14 (0.59), residues: 76 loop : 0.10 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.021 0.002 PHE A 282 TYR 0.018 0.002 TYR A 986 ARG 0.003 0.000 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6414 (mtt180) REVERT: A 230 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7682 (mpt-90) REVERT: A 724 ILE cc_start: 0.7990 (mm) cc_final: 0.7748 (mp) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 1.8897 time to fit residues: 224.6937 Evaluate side-chains 115 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12433 Z= 0.225 Angle : 0.571 10.263 17556 Z= 0.298 Chirality : 0.038 0.212 2020 Planarity : 0.004 0.030 1738 Dihedral : 20.790 164.969 3346 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.75 % Allowed : 10.05 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.23 (0.25), residues: 1097 helix: 1.66 (0.22), residues: 535 sheet: -0.14 (0.58), residues: 76 loop : 0.13 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.021 0.002 PHE A 282 TYR 0.018 0.002 TYR A 986 ARG 0.004 0.000 ARG A1118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.6442 (mtt180) REVERT: A 230 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7648 (mpt-90) REVERT: A 372 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: A 381 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4721 (pp) REVERT: A 724 ILE cc_start: 0.7992 (mm) cc_final: 0.7749 (mp) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 1.8300 time to fit residues: 214.1277 Evaluate side-chains 114 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 0.0470 chunk 72 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 overall best weight: 3.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 12433 Z= 0.349 Angle : 0.663 10.850 17556 Z= 0.343 Chirality : 0.042 0.219 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.880 162.516 3346 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.42 % Allowed : 10.71 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.02 (0.25), residues: 1097 helix: 1.43 (0.22), residues: 536 sheet: -0.04 (0.56), residues: 81 loop : 0.06 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.005 0.001 HIS A 138 PHE 0.026 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.006 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.6399 (mtt180) REVERT: A 230 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7680 (mpt-90) REVERT: A 372 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: A 724 ILE cc_start: 0.7994 (mm) cc_final: 0.7752 (mp) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 1.9008 time to fit residues: 222.0146 Evaluate side-chains 113 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 12433 Z= 0.224 Angle : 0.575 9.928 17556 Z= 0.300 Chirality : 0.038 0.216 2020 Planarity : 0.004 0.031 1738 Dihedral : 20.816 164.468 3346 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.20 % Allowed : 10.93 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.19 (0.25), residues: 1097 helix: 1.63 (0.22), residues: 535 sheet: -0.17 (0.58), residues: 76 loop : 0.10 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.020 0.002 PHE A 282 TYR 0.018 0.002 TYR A 986 ARG 0.002 0.000 ARG A 830 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.6446 (mtt180) REVERT: A 230 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7685 (mpt-90) REVERT: A 372 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: A 724 ILE cc_start: 0.7991 (mm) cc_final: 0.7752 (mp) outliers start: 11 outliers final: 8 residues processed: 107 average time/residue: 1.8827 time to fit residues: 214.2893 Evaluate side-chains 111 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120408 restraints weight = 10050.032| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.18 r_work: 0.3111 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 12433 Z= 0.353 Angle : 0.665 10.779 17556 Z= 0.344 Chirality : 0.042 0.220 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.894 162.365 3346 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.00 (0.25), residues: 1097 helix: 1.42 (0.22), residues: 536 sheet: -0.06 (0.57), residues: 81 loop : 0.04 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.027 0.002 PHE A 282 TYR 0.021 0.003 TYR A 986 ARG 0.006 0.001 ARG A 830 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4495.23 seconds wall clock time: 80 minutes 32.30 seconds (4832.30 seconds total)