Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:35:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_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_11679/04_2023/7a8p_11679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/04_2023/7a8p_11679_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 4.27, per 1000 atoms: 0.58 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: 2.94 Conformation dependent library (CDL) restraints added in 1.0 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: 1.08 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: 2.19 Time building geometry restraints manager: 3.19 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: 4140 23.04 - 46.08: 348 46.08 - 69.11: 30 69.11 - 92.15: 16 92.15 - 115.19: 1 Dihedral angle restraints: 4535 sinusoidal: 1877 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 4532 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: 0.540 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: 3.420 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.720 Find NCS groups from input model: 0.190 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- 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 : 16.097 115.189 2805 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 % 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 *********************** 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 : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 154 average time/residue: 0.2180 time to fit residues: 44.2604 Evaluate side-chains 122 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0807 time to fit residues: 1.3702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 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: 0.7980 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: 0.6982 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.1210 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= 0.191 Angle : 0.521 6.982 10153 Z= 0.253 Chirality : 0.036 0.193 1129 Planarity : 0.004 0.039 1305 Dihedral : 4.076 86.111 1001 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.77 % 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: 2.12 (0.28), residues: 897 helix: 2.12 (0.21), residues: 589 sheet: -0.62 (0.91), residues: 32 loop : 0.19 (0.39), residues: 276 *********************** 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 134 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.779 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.2104 time to fit residues: 36.2617 Evaluate side-chains 116 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1425 time to fit residues: 2.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1786 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= 0.212 Angle : 0.501 8.232 10153 Z= 0.245 Chirality : 0.037 0.252 1129 Planarity : 0.005 0.044 1305 Dihedral : 4.119 78.330 1001 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.02 % 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: 2.26 (0.28), residues: 897 helix: 2.20 (0.21), residues: 587 sheet: -0.89 (0.89), residues: 32 loop : 0.35 (0.38), residues: 278 *********************** 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 134 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.953 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 130 average time/residue: 0.1824 time to fit residues: 32.9099 Evaluate side-chains 111 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0727 time to fit residues: 1.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 624 HIS A 719 GLN ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7482 Z= 0.178 Angle : 0.491 8.352 10153 Z= 0.241 Chirality : 0.036 0.150 1129 Planarity : 0.004 0.043 1305 Dihedral : 4.090 79.131 1001 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.01 % 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: 2.39 (0.28), residues: 897 helix: 2.29 (0.21), residues: 584 sheet: -0.82 (0.90), residues: 32 loop : 0.47 (0.38), residues: 281 *********************** 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 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 121 average time/residue: 0.2004 time to fit residues: 33.7273 Evaluate side-chains 106 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0787 time to fit residues: 1.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 78 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7482 Z= 0.176 Angle : 0.483 8.581 10153 Z= 0.235 Chirality : 0.035 0.143 1129 Planarity : 0.004 0.042 1305 Dihedral : 4.074 77.158 1001 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 1.39 % 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: 2.44 (0.28), residues: 897 helix: 2.31 (0.21), residues: 585 sheet: -0.75 (0.91), residues: 32 loop : 0.52 (0.38), residues: 280 *********************** 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 121 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.895 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 0.1908 time to fit residues: 31.1792 Evaluate side-chains 106 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0740 time to fit residues: 1.9166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS A 893 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2478 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= 0.213 Angle : 0.513 8.836 10153 Z= 0.251 Chirality : 0.036 0.139 1129 Planarity : 0.005 0.062 1305 Dihedral : 4.084 72.780 1001 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.52 % 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: 2.34 (0.29), residues: 897 helix: 2.23 (0.21), residues: 585 sheet: -0.66 (0.97), residues: 32 loop : 0.46 (0.38), residues: 280 *********************** 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 121 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.887 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 0.1851 time to fit residues: 30.2254 Evaluate side-chains 111 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0744 time to fit residues: 1.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7482 Z= 0.172 Angle : 0.497 9.004 10153 Z= 0.241 Chirality : 0.035 0.132 1129 Planarity : 0.005 0.049 1305 Dihedral : 4.071 74.347 1001 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.01 % 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: 2.41 (0.28), residues: 897 helix: 2.30 (0.22), residues: 585 sheet: -0.67 (1.11), residues: 22 loop : 0.40 (0.37), residues: 290 *********************** 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 114 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.919 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 111 average time/residue: 0.2093 time to fit residues: 31.5528 Evaluate side-chains 103 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2254 time to fit residues: 1.8038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 55 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.2688 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= 0.155 Angle : 0.499 8.872 10153 Z= 0.240 Chirality : 0.035 0.125 1129 Planarity : 0.005 0.057 1305 Dihedral : 4.077 75.896 1001 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.51 % 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: 2.39 (0.22), residues: 582 sheet: -0.61 (1.11), residues: 22 loop : 0.43 (0.37), residues: 293 *********************** 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 107 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.789 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 105 average time/residue: 0.2043 time to fit residues: 29.4252 Evaluate side-chains 104 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0849 time to fit residues: 1.6454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 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: 0.7811 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 7482 Z= 0.289 Angle : 0.566 9.645 10153 Z= 0.278 Chirality : 0.038 0.130 1129 Planarity : 0.005 0.054 1305 Dihedral : 4.141 66.267 1001 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.63 % 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: 2.21 (0.29), residues: 897 helix: 2.27 (0.22), residues: 575 sheet: -1.17 (0.96), residues: 27 loop : 0.17 (0.37), residues: 295 *********************** 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 104 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.859 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 103 average time/residue: 0.2089 time to fit residues: 29.4170 Evaluate side-chains 99 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0735 time to fit residues: 1.5349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7482 Z= 0.179 Angle : 0.531 9.533 10153 Z= 0.258 Chirality : 0.035 0.126 1129 Planarity : 0.005 0.055 1305 Dihedral : 4.066 70.731 1001 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.38 % 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: 2.42 (0.29), residues: 897 helix: 2.38 (0.22), residues: 574 sheet: -0.65 (1.09), residues: 22 loop : 0.32 (0.37), residues: 301 ********************** 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 107 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.867 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 104 average time/residue: 0.2161 time to fit residues: 30.2943 Evaluate side-chains 102 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0827 time to fit residues: 1.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119245 restraints weight = 9027.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117479 restraints weight = 7271.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119603 restraints weight = 7119.305| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7482 Z= 0.238 Angle : 0.554 9.486 10153 Z= 0.269 Chirality : 0.037 0.127 1129 Planarity : 0.005 0.051 1305 Dihedral : 4.101 68.021 1001 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 897 helix: 2.27 (0.22), residues: 573 sheet: -0.70 (1.09), residues: 22 loop : 0.24 (0.36), residues: 302 =============================================================================== Job complete usr+sys time: 1499.33 seconds wall clock time: 28 minutes 1.28 seconds (1681.28 seconds total)