Starting phenix.real_space_refine on Sat Apr 6 09:52:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8the_41255/04_2024/8the_41255_neut_updated.pdb" } resolution = 2.5 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= 0.001 sd= 0.065 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 Fe 1 7.16 5 P 2 5.49 5 S 14 5.16 5 C 4812 2.51 5 N 1283 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5629 Classifications: {'peptide': 712} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 680} Chain breaks: 1 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 991 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 248 Unusual residues: {'CTQ': 1, 'HEM': 1} Classifications: {'undetermined': 2, 'water': 67} Link IDs: {None: 68} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.54, per 1000 atoms: 0.59 Number of scatterers: 7682 At special positions: 0 Unit cell: (67.284, 81.168, 121.752, 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) Fe 1 26.01 S 14 16.00 P 2 15.00 O 1570 8.00 N 1283 7.00 C 4812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 13 sheets defined 7.1% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 56 removed outlier: 7.078A pdb=" N PHE A 159 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 136 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 157 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 138 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 155 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 80 Processing sheet with id= C, first strand: chain 'A' and resid 187 through 196 removed outlier: 3.545A pdb=" N GLY A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE A 510 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N VAL A 486 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 387 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP A 297 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 370 through 376 Processing sheet with id= E, first strand: chain 'A' and resid 438 through 440 Processing sheet with id= F, first strand: chain 'A' and resid 522 through 524 removed outlier: 6.434A pdb=" N GLN A 586 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU A 532 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 588 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 570 through 572 Processing sheet with id= H, first strand: chain 'H' and resid 5 through 10 Processing sheet with id= I, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.583A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.633A pdb=" N TYR H 119 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= L, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.711A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA L 14 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU L 106 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.167A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1014 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: 2.82 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.33: 2327 1.33 - 1.51: 2672 1.51 - 1.69: 2769 1.69 - 1.87: 24 1.87 - 2.05: 4 Bond restraints: 7796 Sorted by residual: bond pdb=" C49 CTQ A 802 " pdb=" O56 CTQ A 802 " ideal model delta sigma weight residual 1.427 1.555 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C GLU A 307 " pdb=" O GLU A 307 " ideal model delta sigma weight residual 1.235 1.155 0.081 1.28e-02 6.10e+03 3.97e+01 bond pdb=" C TYR A 702 " pdb=" O TYR A 702 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.15e-02 7.56e+03 3.01e+01 bond pdb=" C44 CTQ A 802 " pdb=" O45 CTQ A 802 " ideal model delta sigma weight residual 1.442 1.537 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C17 CTQ A 802 " pdb=" C29 CTQ A 802 " ideal model delta sigma weight residual 1.558 1.650 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7791 not shown) Histogram of bond angle deviations from ideal: 89.30 - 106.81: 241 106.81 - 124.32: 10086 124.32 - 141.83: 246 141.83 - 159.34: 0 159.34 - 176.85: 2 Bond angle restraints: 10575 Sorted by residual: angle pdb=" CA ASP A 698 " pdb=" CB ASP A 698 " pdb=" CG ASP A 698 " ideal model delta sigma weight residual 112.60 119.87 -7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" C GLU A 75 " pdb=" CA GLU A 75 " pdb=" CB GLU A 75 " ideal model delta sigma weight residual 110.44 115.58 -5.14 9.00e-01 1.23e+00 3.26e+01 angle pdb=" CG7 CTQ A 802 " pdb=" CG9 CTQ A 802 " pdb=" CGA CTQ A 802 " ideal model delta sigma weight residual 109.45 125.18 -15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N TYR A 74 " pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " ideal model delta sigma weight residual 110.98 102.34 8.64 1.65e+00 3.67e-01 2.74e+01 angle pdb=" CA ASP A 302 " pdb=" CB ASP A 302 " pdb=" CG ASP A 302 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 ... (remaining 10570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.48: 4434 29.48 - 58.96: 86 58.96 - 88.43: 18 88.43 - 117.91: 11 117.91 - 147.39: 6 Dihedral angle restraints: 4555 sinusoidal: 1854 harmonic: 2701 Sorted by residual: dihedral pdb=" C17 CTQ A 802 " pdb=" C14 CTQ A 802 " pdb=" O16 CTQ A 802 " pdb=" O15 CTQ A 802 " ideal model delta sinusoidal sigma weight residual -29.99 117.40 -147.39 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CF8 CTQ A 802 " pdb=" CFA CTQ A 802 " pdb=" CFB CTQ A 802 " pdb=" CFC CTQ A 802 " ideal model delta sinusoidal sigma weight residual 153.96 -65.52 -140.52 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CD ARG A 73 " pdb=" NE ARG A 73 " pdb=" CZ ARG A 73 " pdb=" NH1 ARG A 73 " ideal model delta sinusoidal sigma weight residual 0.00 36.52 -36.52 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 4552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1075 0.166 - 0.332: 11 0.332 - 0.498: 4 0.498 - 0.664: 1 0.664 - 0.830: 2 Chirality restraints: 1093 Sorted by residual: chirality pdb=" C34 CTQ A 802 " pdb=" C33 CTQ A 802 " pdb=" C35 CTQ A 802 " pdb=" NG6 CTQ A 802 " both_signs ideal model delta sigma weight residual False 2.57 1.74 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CEZ CTQ A 802 " pdb=" CEY CTQ A 802 " pdb=" CF0 CTQ A 802 " pdb=" NF7 CTQ A 802 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CEY CTQ A 802 " pdb=" CEX CTQ A 802 " pdb=" CEZ CTQ A 802 " pdb=" OFO CTQ A 802 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.40e+00 ... (remaining 1090 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 73 " -0.642 9.50e-02 1.11e+02 2.88e-01 5.05e+01 pdb=" NE ARG A 73 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 73 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 73 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 73 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 700 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C SER A 700 " 0.049 2.00e-02 2.50e+03 pdb=" O SER A 700 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 701 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C34 CTQ A 802 " -0.022 2.00e-02 2.50e+03 1.91e-02 4.54e+00 pdb=" CG7 CTQ A 802 " 0.023 2.00e-02 2.50e+03 pdb=" CG9 CTQ A 802 " -0.022 2.00e-02 2.50e+03 pdb=" NG6 CTQ A 802 " 0.019 2.00e-02 2.50e+03 pdb=" OG8 CTQ A 802 " 0.002 2.00e-02 2.50e+03 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 132 2.64 - 3.21: 6259 3.21 - 3.77: 12023 3.77 - 4.34: 18202 4.34 - 4.90: 29671 Nonbonded interactions: 66287 Sorted by model distance: nonbonded pdb=" OE1 GLN L 91 " pdb=" O HOH L 301 " model vdw 2.076 2.440 nonbonded pdb=" OE1 GLU H 4 " pdb=" O HOH H 301 " model vdw 2.161 2.440 nonbonded pdb=" OG1 THR A 354 " pdb=" OG1 THR A 401 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASP A 424 " pdb=" O HOH A 901 " model vdw 2.207 2.440 nonbonded pdb=" ND2 ASN A 64 " pdb=" O HOH A 902 " model vdw 2.232 2.520 ... (remaining 66282 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.020 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.006 0.128 7796 Z= 0.386 Angle : 0.786 15.730 10575 Z= 0.402 Chirality : 0.064 0.830 1093 Planarity : 0.009 0.288 1367 Dihedral : 14.879 147.390 2851 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.64 % Allowed : 2.68 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 938 helix: -1.32 (0.83), residues: 38 sheet: 1.41 (0.23), residues: 490 loop : 0.22 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 762 HIS 0.002 0.001 HIS A 206 PHE 0.011 0.001 PHE H 32 TYR 0.031 0.001 TYR A 702 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 164 SER cc_start: 0.7852 (p) cc_final: 0.7562 (m) REVERT: A 289 MET cc_start: 0.8119 (mtp) cc_final: 0.7730 (mtp) REVERT: A 323 ASP cc_start: 0.8437 (m-30) cc_final: 0.8124 (m-30) REVERT: A 478 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 636 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 675 ASP cc_start: 0.8815 (t0) cc_final: 0.8452 (t0) REVERT: A 677 SER cc_start: 0.8638 (p) cc_final: 0.8381 (p) REVERT: A 708 ASP cc_start: 0.7950 (m-30) cc_final: 0.7556 (p0) REVERT: A 737 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: H 16 GLN cc_start: 0.7146 (tt0) cc_final: 0.6848 (tm-30) REVERT: H 86 MET cc_start: 0.9174 (mtp) cc_final: 0.8896 (mtm) outliers start: 5 outliers final: 1 residues processed: 163 average time/residue: 1.4610 time to fit residues: 250.1367 Evaluate side-chains 118 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 737 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS A 301 ASN A 543 GLN A 586 GLN H 6 GLN L 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7796 Z= 0.214 Angle : 0.594 8.204 10575 Z= 0.296 Chirality : 0.049 0.464 1093 Planarity : 0.004 0.040 1367 Dihedral : 15.908 129.476 1168 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 9.06 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 938 helix: -1.15 (0.82), residues: 38 sheet: 1.49 (0.23), residues: 469 loop : 0.19 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.004 0.001 HIS A 314 PHE 0.014 0.002 PHE A 374 TYR 0.013 0.001 TYR A 239 ARG 0.006 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.824 Fit side-chains REVERT: A 335 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8654 (pttp) REVERT: A 356 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: A 478 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 636 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 675 ASP cc_start: 0.8866 (t0) cc_final: 0.8612 (t0) REVERT: A 677 SER cc_start: 0.8672 (p) cc_final: 0.8416 (p) REVERT: A 698 ASP cc_start: 0.9003 (m-30) cc_final: 0.8752 (m-30) REVERT: A 708 ASP cc_start: 0.7682 (m-30) cc_final: 0.7291 (p0) REVERT: A 737 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: H 86 MET cc_start: 0.9186 (mtp) cc_final: 0.8923 (mtm) outliers start: 20 outliers final: 10 residues processed: 126 average time/residue: 1.4234 time to fit residues: 191.6443 Evaluate side-chains 122 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS A 301 ASN H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7796 Z= 0.237 Angle : 0.597 7.582 10575 Z= 0.298 Chirality : 0.049 0.436 1093 Planarity : 0.004 0.051 1367 Dihedral : 15.153 117.640 1168 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.06 % Allowed : 9.31 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 938 helix: -1.22 (0.80), residues: 38 sheet: 1.29 (0.23), residues: 480 loop : 0.27 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.005 0.001 HIS A 314 PHE 0.015 0.002 PHE H 32 TYR 0.013 0.001 TYR A 239 ARG 0.007 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.936 Fit side-chains REVERT: A 171 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7604 (mptt) REVERT: A 289 MET cc_start: 0.8238 (mtp) cc_final: 0.7891 (mtp) REVERT: A 335 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8597 (pttp) REVERT: A 478 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 554 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: A 636 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8334 (mm-30) REVERT: A 675 ASP cc_start: 0.8922 (t0) cc_final: 0.8624 (t0) REVERT: A 677 SER cc_start: 0.8693 (p) cc_final: 0.8448 (p) REVERT: A 708 ASP cc_start: 0.7681 (m-30) cc_final: 0.7399 (m-30) REVERT: A 737 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: H 49 GLU cc_start: 0.8946 (tt0) cc_final: 0.8693 (tt0) REVERT: H 86 MET cc_start: 0.9147 (mtp) cc_final: 0.8919 (mtm) outliers start: 24 outliers final: 14 residues processed: 123 average time/residue: 1.3888 time to fit residues: 180.0824 Evaluate side-chains 129 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS A 301 ASN H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7796 Z= 0.243 Angle : 0.591 7.252 10575 Z= 0.296 Chirality : 0.048 0.426 1093 Planarity : 0.004 0.053 1367 Dihedral : 14.518 117.643 1168 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.19 % Allowed : 10.33 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 938 helix: -1.16 (0.81), residues: 38 sheet: 1.18 (0.23), residues: 481 loop : 0.25 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.005 0.001 HIS A 314 PHE 0.014 0.002 PHE H 32 TYR 0.013 0.001 TYR A 239 ARG 0.007 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.865 Fit side-chains REVERT: A 171 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7617 (mptt) REVERT: A 335 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8578 (pttp) REVERT: A 356 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: A 478 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 554 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: A 636 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 675 ASP cc_start: 0.8937 (t0) cc_final: 0.8638 (t0) REVERT: A 677 SER cc_start: 0.8698 (p) cc_final: 0.8484 (p) REVERT: A 708 ASP cc_start: 0.7683 (m-30) cc_final: 0.7362 (m-30) REVERT: A 737 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: H 49 GLU cc_start: 0.8941 (tt0) cc_final: 0.8694 (tt0) REVERT: H 86 MET cc_start: 0.9107 (mtp) cc_final: 0.8837 (mtm) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 1.3946 time to fit residues: 174.9659 Evaluate side-chains 124 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS A 301 ASN H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7796 Z= 0.189 Angle : 0.548 6.916 10575 Z= 0.276 Chirality : 0.046 0.391 1093 Planarity : 0.004 0.052 1367 Dihedral : 13.932 117.950 1168 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.93 % Allowed : 10.46 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 938 helix: -1.03 (0.82), residues: 38 sheet: 1.12 (0.23), residues: 483 loop : 0.32 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 239 ARG 0.008 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.834 Fit side-chains REVERT: A 171 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7655 (mptt) REVERT: A 342 GLU cc_start: 0.8811 (pt0) cc_final: 0.8455 (pt0) REVERT: A 356 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: A 478 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 554 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: A 636 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 675 ASP cc_start: 0.8881 (t0) cc_final: 0.8648 (t0) REVERT: A 708 ASP cc_start: 0.7602 (m-30) cc_final: 0.7209 (m-30) REVERT: A 737 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: H 49 GLU cc_start: 0.8939 (tt0) cc_final: 0.8703 (tt0) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 1.3750 time to fit residues: 176.9940 Evaluate side-chains 127 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7796 Z= 0.260 Angle : 0.598 7.392 10575 Z= 0.299 Chirality : 0.049 0.414 1093 Planarity : 0.004 0.053 1367 Dihedral : 13.986 118.402 1168 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.44 % Allowed : 10.33 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 938 helix: -1.11 (0.80), residues: 38 sheet: 1.10 (0.23), residues: 481 loop : 0.25 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.015 0.002 PHE H 32 TYR 0.013 0.001 TYR A 239 ARG 0.008 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.891 Fit side-chains REVERT: A 171 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7630 (mptt) REVERT: A 417 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: A 478 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 554 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: A 636 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 675 ASP cc_start: 0.8933 (t0) cc_final: 0.8636 (t0) REVERT: A 708 ASP cc_start: 0.7598 (m-30) cc_final: 0.7184 (m-30) REVERT: A 737 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: H 49 GLU cc_start: 0.8943 (tt0) cc_final: 0.8687 (tt0) REVERT: H 92 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7854 (pm20) outliers start: 27 outliers final: 19 residues processed: 117 average time/residue: 1.3190 time to fit residues: 163.4097 Evaluate side-chains 128 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7796 Z= 0.339 Angle : 0.646 8.644 10575 Z= 0.322 Chirality : 0.051 0.424 1093 Planarity : 0.005 0.055 1367 Dihedral : 14.148 118.862 1168 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.44 % Allowed : 10.97 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 938 helix: -1.27 (0.77), residues: 38 sheet: 1.03 (0.22), residues: 483 loop : 0.21 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 297 HIS 0.005 0.001 HIS A 314 PHE 0.018 0.002 PHE H 32 TYR 0.014 0.002 TYR L 87 ARG 0.008 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.870 Fit side-chains REVERT: A 171 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7614 (mptt) REVERT: A 356 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: A 417 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: A 422 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9176 (p90) REVERT: A 554 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: A 708 ASP cc_start: 0.7633 (m-30) cc_final: 0.7206 (m-30) REVERT: A 737 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: H 49 GLU cc_start: 0.8985 (tt0) cc_final: 0.8739 (tt0) REVERT: H 92 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7902 (pm20) outliers start: 27 outliers final: 16 residues processed: 116 average time/residue: 1.3469 time to fit residues: 164.9876 Evaluate side-chains 123 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7796 Z= 0.207 Angle : 0.565 7.017 10575 Z= 0.284 Chirality : 0.047 0.372 1093 Planarity : 0.004 0.055 1367 Dihedral : 13.674 118.507 1167 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.32 % Allowed : 11.35 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 938 helix: -1.03 (0.81), residues: 38 sheet: 1.06 (0.23), residues: 481 loop : 0.23 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 239 ARG 0.009 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.914 Fit side-chains REVERT: A 131 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7982 (t0) REVERT: A 171 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7657 (mptt) REVERT: A 342 GLU cc_start: 0.8843 (pt0) cc_final: 0.8484 (pt0) REVERT: A 417 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: A 422 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.9065 (p90) REVERT: A 554 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: A 636 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8355 (mm-30) REVERT: A 675 ASP cc_start: 0.8912 (t0) cc_final: 0.8670 (t0) REVERT: A 708 ASP cc_start: 0.7601 (m-30) cc_final: 0.7174 (m-30) REVERT: A 737 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: L 43 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8104 (mmmm) outliers start: 26 outliers final: 17 residues processed: 122 average time/residue: 1.3853 time to fit residues: 178.6788 Evaluate side-chains 128 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7796 Z= 0.201 Angle : 0.562 6.919 10575 Z= 0.282 Chirality : 0.046 0.358 1093 Planarity : 0.004 0.054 1367 Dihedral : 13.527 119.689 1167 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.57 % Allowed : 11.22 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 938 helix: -0.97 (0.81), residues: 38 sheet: 1.03 (0.23), residues: 480 loop : 0.27 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 239 ARG 0.008 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.975 Fit side-chains REVERT: A 131 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7983 (t0) REVERT: A 171 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7660 (mptt) REVERT: A 342 GLU cc_start: 0.8845 (pt0) cc_final: 0.8477 (pt0) REVERT: A 417 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: A 422 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9103 (p90) REVERT: A 554 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: A 708 ASP cc_start: 0.7597 (m-30) cc_final: 0.7242 (m-30) REVERT: A 737 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: L 43 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8098 (mmmm) outliers start: 28 outliers final: 19 residues processed: 120 average time/residue: 1.3388 time to fit residues: 169.6622 Evaluate side-chains 129 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7796 Z= 0.194 Angle : 0.558 6.956 10575 Z= 0.280 Chirality : 0.046 0.355 1093 Planarity : 0.004 0.054 1367 Dihedral : 13.407 120.331 1167 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.32 % Allowed : 11.73 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 938 helix: -0.93 (0.82), residues: 38 sheet: 1.06 (0.23), residues: 479 loop : 0.29 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 239 ARG 0.009 0.000 ARG L 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.877 Fit side-chains REVERT: A 131 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7983 (t0) REVERT: A 171 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7664 (mptt) REVERT: A 342 GLU cc_start: 0.8831 (pt0) cc_final: 0.8465 (pt0) REVERT: A 417 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: A 422 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9087 (p90) REVERT: A 554 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: A 708 ASP cc_start: 0.7597 (m-30) cc_final: 0.7242 (m-30) REVERT: A 737 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: L 43 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8104 (mmmm) outliers start: 26 outliers final: 20 residues processed: 117 average time/residue: 1.3721 time to fit residues: 169.3442 Evaluate side-chains 128 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 221 HIS H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.099899 restraints weight = 7530.926| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.00 r_work: 0.2949 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7796 Z= 0.201 Angle : 0.564 6.893 10575 Z= 0.282 Chirality : 0.046 0.352 1093 Planarity : 0.004 0.054 1367 Dihedral : 13.369 120.996 1167 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.32 % Allowed : 11.73 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 938 helix: -0.91 (0.81), residues: 38 sheet: 1.07 (0.23), residues: 479 loop : 0.28 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 314 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 239 ARG 0.009 0.000 ARG L 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.38 seconds wall clock time: 62 minutes 51.69 seconds (3771.69 seconds total)