Starting phenix.real_space_refine on Mon Mar 11 06:09:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/03_2024/7a8p_11679_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.003 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 S 46 5.16 5 Cl 1 4.86 5 C 4669 2.51 5 N 1304 2.21 5 O 1284 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 819": "OD1" <-> "OD2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ASP 876": "OD1" <-> "OD2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A TYR 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1128": "OD1" <-> "OD2" Residue "A PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A ASP 1218": "OD1" <-> "OD2" Residue "A GLU 1220": "OE1" <-> "OE2" Residue "A TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7305 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7305 Unusual residues: {'R4Q': 1} Inner-chain residues flagged as termini: ['pdbres="SER A1230 "'] Classifications: {'peptide': 911, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 59, 'TRANS': 851, None: 1} Not linked: pdbres="SER A1230 " pdbres="R4Q A1301 " Chain breaks: 6 Time building chain proxies: 4.17, per 1000 atoms: 0.57 Number of scatterers: 7305 At special positions: 0 Unit cell: (77.562, 97.578, 110.922, 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) Cl 1 17.00 S 46 16.00 F 1 9.00 O 1284 8.00 N 1304 7.00 C 4669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 330 through 336 removed outlier: 4.167A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.595A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 427 through 462 removed outlier: 3.719A pdb=" N ARG A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 497 through 519 Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.683A pdb=" N LYS A 532 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 689 through 703 removed outlier: 4.481A pdb=" N GLY A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 857 through 876 removed outlier: 5.336A pdb=" N ASP A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 887 No H-bonds generated for 'chain 'A' and resid 885 through 887' Processing helix chain 'A' and resid 891 through 906 Processing helix chain 'A' and resid 926 through 935 Processing helix chain 'A' and resid 938 through 943 Processing helix chain 'A' and resid 955 through 973 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 987 through 999 Processing helix chain 'A' and resid 1007 through 1017 removed outlier: 3.586A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 5.244A pdb=" N TRP A1026 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1063 Processing helix chain 'A' and resid 1114 through 1142 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1160 through 1176 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1219 through 1224 Processing sheet with id= A, first strand: chain 'A' and resid 411 through 415 Processing sheet with id= B, first strand: chain 'A' and resid 607 through 609 removed outlier: 3.515A pdb=" N TYR A 607 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 622 " --> pdb=" O TYR A 607 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 620 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 707 through 709 Processing sheet with id= D, first strand: chain 'A' and resid 919 through 921 Processing sheet with id= E, first strand: chain 'A' and resid 1069 through 1071 385 hydrogen bonds defined for protein. 1083 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: 2.12 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1746 1.33 - 1.45: 1433 1.45 - 1.57: 4230 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 7482 Sorted by residual: bond pdb=" C21 R4Q A1301 " pdb=" O20 R4Q A1301 " ideal model delta sigma weight residual 1.498 1.379 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C02 R4Q A1301 " pdb=" C23 R4Q A1301 " ideal model delta sigma weight residual 1.528 1.642 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C08 R4Q A1301 " pdb=" C17 R4Q A1301 " ideal model delta sigma weight residual 1.449 1.348 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " ideal model delta sigma weight residual 1.398 1.483 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C12 R4Q A1301 " pdb=" F13 R4Q A1301 " ideal model delta sigma weight residual 1.364 1.281 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 7477 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 309 107.13 - 113.84: 4165 113.84 - 120.54: 3103 120.54 - 127.25: 2453 127.25 - 133.95: 123 Bond angle restraints: 10153 Sorted by residual: angle pdb=" C09 R4Q A1301 " pdb=" C15 R4Q A1301 " pdb="CL1 R4Q A1301 " ideal model delta sigma weight residual 134.09 119.08 15.01 3.00e+00 1.11e-01 2.50e+01 angle pdb=" C14 R4Q A1301 " pdb=" C15 R4Q A1301 " pdb="CL1 R4Q A1301 " ideal model delta sigma weight residual 105.54 118.39 -12.85 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C23 R4Q A1301 " pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " ideal model delta sigma weight residual 109.47 117.54 -8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA PRO A 423 " pdb=" C PRO A 423 " pdb=" N SER A 424 " ideal model delta sigma weight residual 114.74 117.22 -2.48 1.03e+00 9.43e-01 5.79e+00 angle pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " pdb=" C04 R4Q A1301 " ideal model delta sigma weight residual 113.89 120.18 -6.29 3.00e+00 1.11e-01 4.39e+00 ... (remaining 10148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 4141 23.04 - 46.08: 352 46.08 - 69.11: 30 69.11 - 92.15: 16 92.15 - 115.19: 1 Dihedral angle restraints: 4540 sinusoidal: 1882 harmonic: 2658 Sorted by residual: dihedral pdb=" C28 R4Q A1301 " pdb=" C26 R4Q A1301 " pdb=" C27 R4Q A1301 " pdb=" N25 R4Q A1301 " ideal model delta sinusoidal sigma weight residual 53.84 -61.35 115.19 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " pdb=" OE1 GLU A 495 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C26 R4Q A1301 " pdb=" C27 R4Q A1301 " pdb=" C28 R4Q A1301 " pdb=" C29 R4Q A1301 " ideal model delta sinusoidal sigma weight residual 53.22 -32.84 86.06 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 4537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 865 0.031 - 0.062: 178 0.062 - 0.093: 57 0.093 - 0.123: 25 0.123 - 0.154: 4 Chirality restraints: 1129 Sorted by residual: chirality pdb=" C02 R4Q A1301 " pdb=" C01 R4Q A1301 " pdb=" C23 R4Q A1301 " pdb=" O03 R4Q A1301 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" C29 R4Q A1301 " pdb=" C28 R4Q A1301 " pdb=" C30 R4Q A1301 " pdb=" C33 R4Q A1301 " both_signs ideal model delta sigma weight residual False -2.70 -2.84 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA VAL A1211 " pdb=" N VAL A1211 " pdb=" C VAL A1211 " pdb=" CB VAL A1211 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1126 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 624 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 625 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1119 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-01 pdb=" N PRO A1120 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.08e-01 pdb=" N PRO A 240 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.012 5.00e-02 4.00e+02 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 164 2.71 - 3.26: 7634 3.26 - 3.81: 12011 3.81 - 4.35: 14364 4.35 - 4.90: 24784 Nonbonded interactions: 58957 Sorted by model distance: nonbonded pdb=" O TYR A1082 " pdb=" NE2 GLN A1115 " model vdw 2.165 2.520 nonbonded pdb=" O VAL A1001 " pdb=" OG1 THR A1002 " model vdw 2.178 2.440 nonbonded pdb=" OE1 GLN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.246 2.520 nonbonded pdb=" OH TYR A 530 " pdb=" O PRO A 651 " model vdw 2.279 2.440 nonbonded pdb=" N GLU A 545 " pdb=" OE1 GLU A 545 " model vdw 2.285 2.520 ... (remaining 58952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 3.150 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.060 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.004 0.119 7482 Z= 0.255 Angle : 0.530 15.011 10153 Z= 0.253 Chirality : 0.032 0.154 1129 Planarity : 0.003 0.034 1305 Dihedral : 16.131 115.189 2810 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.63 % Allowed : 4.30 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 897 helix: 1.44 (0.20), residues: 585 sheet: -1.19 (0.84), residues: 32 loop : -0.77 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1026 HIS 0.006 0.001 HIS A 243 PHE 0.006 0.001 PHE A1146 TYR 0.008 0.001 TYR A1140 ARG 0.009 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 530 TYR cc_start: 0.7928 (t80) cc_final: 0.7587 (t80) REVERT: A 966 PHE cc_start: 0.8012 (m-10) cc_final: 0.7794 (m-10) REVERT: A 1027 GLU cc_start: 0.6864 (mp0) cc_final: 0.6600 (mp0) outliers start: 5 outliers final: 1 residues processed: 154 average time/residue: 0.2119 time to fit residues: 42.9726 Evaluate side-chains 122 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 488 GLN A 624 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7482 Z= 0.182 Angle : 0.511 6.802 10153 Z= 0.248 Chirality : 0.036 0.194 1129 Planarity : 0.004 0.038 1305 Dihedral : 4.877 83.846 1008 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.90 % Allowed : 10.24 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.28), residues: 897 helix: 2.15 (0.21), residues: 589 sheet: -0.63 (0.91), residues: 32 loop : 0.18 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1026 HIS 0.003 0.001 HIS A1175 PHE 0.009 0.001 PHE A 721 TYR 0.014 0.001 TYR A 264 ARG 0.006 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.836 Fit side-chains REVERT: A 286 MET cc_start: 0.7542 (mmt) cc_final: 0.7097 (tpp) REVERT: A 509 PHE cc_start: 0.7899 (t80) cc_final: 0.7680 (t80) REVERT: A 530 TYR cc_start: 0.7925 (t80) cc_final: 0.7442 (t80) REVERT: A 589 MET cc_start: 0.6869 (ttp) cc_final: 0.6650 (ttp) REVERT: A 884 TRP cc_start: 0.7665 (t60) cc_final: 0.7252 (t60) REVERT: A 966 PHE cc_start: 0.7995 (m-10) cc_final: 0.7738 (m-10) outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.1988 time to fit residues: 35.3030 Evaluate side-chains 118 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A 893 GLN A 921 GLN ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.030 7482 Z= 0.187 Angle : 0.490 8.119 10153 Z= 0.239 Chirality : 0.036 0.232 1129 Planarity : 0.004 0.043 1305 Dihedral : 4.920 82.806 1008 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.28 % Allowed : 13.27 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 897 helix: 2.27 (0.21), residues: 587 sheet: -0.89 (0.89), residues: 32 loop : 0.31 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.004 0.001 HIS A1138 PHE 0.010 0.001 PHE A 721 TYR 0.012 0.001 TYR A 264 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.817 Fit side-chains REVERT: A 509 PHE cc_start: 0.7925 (t80) cc_final: 0.7696 (t80) REVERT: A 530 TYR cc_start: 0.7895 (t80) cc_final: 0.7358 (t80) REVERT: A 624 HIS cc_start: 0.6712 (t-90) cc_final: 0.6484 (t-170) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.1872 time to fit residues: 32.5090 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.0870 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7482 Z= 0.148 Angle : 0.474 8.437 10153 Z= 0.232 Chirality : 0.035 0.170 1129 Planarity : 0.004 0.042 1305 Dihedral : 4.923 85.409 1008 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.15 % Allowed : 15.30 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.28), residues: 897 helix: 2.36 (0.21), residues: 586 sheet: -0.91 (0.87), residues: 32 loop : 0.49 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 884 HIS 0.003 0.001 HIS A1138 PHE 0.017 0.001 PHE A 229 TYR 0.010 0.001 TYR A 282 ARG 0.008 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7760 (mm) REVERT: A 509 PHE cc_start: 0.7877 (t80) cc_final: 0.7663 (t80) REVERT: A 530 TYR cc_start: 0.7927 (t80) cc_final: 0.7372 (t80) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.1914 time to fit residues: 32.7627 Evaluate side-chains 113 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 0.0020 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7482 Z= 0.177 Angle : 0.487 8.647 10153 Z= 0.237 Chirality : 0.036 0.171 1129 Planarity : 0.004 0.042 1305 Dihedral : 4.854 81.067 1008 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 15.17 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.28), residues: 897 helix: 2.35 (0.21), residues: 587 sheet: -0.80 (0.91), residues: 32 loop : 0.55 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 884 HIS 0.006 0.001 HIS A 250 PHE 0.017 0.001 PHE A 229 TYR 0.006 0.001 TYR A 931 ARG 0.012 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.862 Fit side-chains REVERT: A 239 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 286 MET cc_start: 0.8550 (tpp) cc_final: 0.8143 (mmm) REVERT: A 509 PHE cc_start: 0.7864 (t80) cc_final: 0.7592 (t80) REVERT: A 530 TYR cc_start: 0.7897 (t80) cc_final: 0.7328 (t80) REVERT: A 771 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5479 (pt0) REVERT: A 999 TYR cc_start: 0.7898 (m-80) cc_final: 0.7502 (m-80) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.1834 time to fit residues: 29.8592 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7482 Z= 0.182 Angle : 0.485 8.818 10153 Z= 0.237 Chirality : 0.036 0.173 1129 Planarity : 0.004 0.044 1305 Dihedral : 4.770 77.932 1008 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.03 % Allowed : 15.42 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.29), residues: 897 helix: 2.37 (0.22), residues: 587 sheet: -0.61 (0.94), residues: 32 loop : 0.58 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.006 0.001 HIS A 250 PHE 0.016 0.001 PHE A 229 TYR 0.006 0.001 TYR A 931 ARG 0.009 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 509 PHE cc_start: 0.7863 (t80) cc_final: 0.7582 (t80) REVERT: A 530 TYR cc_start: 0.7845 (t80) cc_final: 0.7313 (t80) REVERT: A 771 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.5687 (pt0) REVERT: A 999 TYR cc_start: 0.8025 (m-80) cc_final: 0.7822 (m-80) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1889 time to fit residues: 31.4293 Evaluate side-chains 120 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7482 Z= 0.193 Angle : 0.503 9.078 10153 Z= 0.245 Chirality : 0.036 0.171 1129 Planarity : 0.005 0.064 1305 Dihedral : 4.728 76.290 1008 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.91 % Allowed : 17.07 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.29), residues: 897 helix: 2.40 (0.22), residues: 587 sheet: -0.59 (0.97), residues: 32 loop : 0.58 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.004 0.001 HIS A1138 PHE 0.016 0.001 PHE A 229 TYR 0.006 0.001 TYR A 931 ARG 0.010 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7724 (mm) REVERT: A 509 PHE cc_start: 0.7914 (t80) cc_final: 0.7654 (t80) REVERT: A 530 TYR cc_start: 0.7865 (t80) cc_final: 0.7309 (t80) REVERT: A 771 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: A 999 TYR cc_start: 0.8071 (m-80) cc_final: 0.7827 (m-80) outliers start: 23 outliers final: 18 residues processed: 120 average time/residue: 0.1924 time to fit residues: 31.5360 Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7482 Z= 0.182 Angle : 0.499 9.088 10153 Z= 0.243 Chirality : 0.035 0.167 1129 Planarity : 0.004 0.054 1305 Dihedral : 4.706 75.991 1008 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.78 % Allowed : 17.83 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.29), residues: 897 helix: 2.44 (0.22), residues: 585 sheet: -0.58 (0.95), residues: 32 loop : 0.54 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.003 0.001 HIS A1138 PHE 0.009 0.001 PHE A 802 TYR 0.006 0.001 TYR A 282 ARG 0.010 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.873 Fit side-chains REVERT: A 239 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 286 MET cc_start: 0.8411 (tpp) cc_final: 0.8113 (mmm) REVERT: A 509 PHE cc_start: 0.7913 (t80) cc_final: 0.7698 (t80) REVERT: A 530 TYR cc_start: 0.7845 (t80) cc_final: 0.7284 (t80) REVERT: A 771 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5778 (pt0) REVERT: A 999 TYR cc_start: 0.8077 (m-80) cc_final: 0.7833 (m-80) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1926 time to fit residues: 31.4846 Evaluate side-chains 121 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 624 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7482 Z= 0.178 Angle : 0.509 9.283 10153 Z= 0.250 Chirality : 0.035 0.167 1129 Planarity : 0.005 0.060 1305 Dihedral : 4.705 76.426 1008 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.16 % Allowed : 17.83 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.29), residues: 897 helix: 2.42 (0.22), residues: 585 sheet: -0.57 (0.96), residues: 32 loop : 0.54 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.007 0.001 HIS A 624 PHE 0.017 0.001 PHE A 229 TYR 0.007 0.001 TYR A 282 ARG 0.012 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.855 Fit side-chains REVERT: A 239 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 286 MET cc_start: 0.8410 (tpp) cc_final: 0.8086 (mmm) REVERT: A 509 PHE cc_start: 0.7879 (t80) cc_final: 0.7651 (t80) REVERT: A 530 TYR cc_start: 0.7844 (t80) cc_final: 0.7287 (t80) REVERT: A 771 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.5888 (pt0) REVERT: A 999 TYR cc_start: 0.8078 (m-80) cc_final: 0.7866 (m-80) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.2005 time to fit residues: 32.9661 Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 624 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7482 Z= 0.228 Angle : 0.536 9.403 10153 Z= 0.262 Chirality : 0.036 0.173 1129 Planarity : 0.005 0.056 1305 Dihedral : 4.682 72.909 1008 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.53 % Allowed : 18.71 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 897 helix: 2.42 (0.22), residues: 577 sheet: -0.75 (1.08), residues: 22 loop : 0.41 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 707 HIS 0.009 0.001 HIS A 624 PHE 0.010 0.001 PHE A 230 TYR 0.006 0.001 TYR A 931 ARG 0.012 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.861 Fit side-chains REVERT: A 239 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7786 (mm) REVERT: A 268 MET cc_start: 0.8663 (mmm) cc_final: 0.8359 (mmm) REVERT: A 286 MET cc_start: 0.8420 (tpp) cc_final: 0.8061 (mmm) REVERT: A 456 LEU cc_start: 0.7612 (mt) cc_final: 0.7331 (mt) REVERT: A 530 TYR cc_start: 0.7806 (t80) cc_final: 0.7263 (t80) REVERT: A 771 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.5821 (pt0) REVERT: A 999 TYR cc_start: 0.8099 (m-80) cc_final: 0.7869 (m-80) REVERT: A 1038 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8524 (tttp) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.1921 time to fit residues: 30.4307 Evaluate side-chains 120 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117610 restraints weight = 9010.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116532 restraints weight = 7299.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118435 restraints weight = 7376.396| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7482 Z= 0.293 Angle : 0.578 9.567 10153 Z= 0.283 Chirality : 0.038 0.188 1129 Planarity : 0.005 0.053 1305 Dihedral : 4.700 67.794 1008 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.78 % Allowed : 18.58 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.29), residues: 897 helix: 2.25 (0.22), residues: 575 sheet: -0.85 (1.05), residues: 22 loop : 0.19 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 707 HIS 0.026 0.002 HIS A 624 PHE 0.014 0.002 PHE A 229 TYR 0.009 0.001 TYR A 282 ARG 0.010 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.36 seconds wall clock time: 29 minutes 26.28 seconds (1766.28 seconds total)