Starting phenix.real_space_refine on Tue Feb 13 19:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rd7_24414/02_2024/7rd7_24414_updated.pdb" } resolution = 3.08 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 37 5.16 5 C 4762 2.51 5 N 1220 2.21 5 O 1375 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 167": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A ARG 930": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7400 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7400 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 929, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 902, None: 2} Not linked: pdbres="SER A1141 " pdbres="ALF A1201 " Not linked: pdbres="ALF A1201 " pdbres=" MG A1202 " Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.38, per 1000 atoms: 0.59 Number of scatterers: 7400 At special positions: 0 Unit cell: (74.34, 82.6, 140.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 37 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1375 8.00 N 1220 7.00 C 4762 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 9 sheets defined 43.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 197 through 210 removed outlier: 4.290A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 249 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 406 through 433 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 455 through 476 removed outlier: 3.966A pdb=" N ARG A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.797A pdb=" N SER A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 667 through 670 No H-bonds generated for 'chain 'A' and resid 667 through 670' Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.964A pdb=" N GLU A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 757 through 765 Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 859 through 872 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.530A pdb=" N VAL A 887 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER A 888 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 889 " --> pdb=" O ASP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 919 through 926 removed outlier: 3.509A pdb=" N THR A 922 " --> pdb=" O CYS A 919 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 926 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 960 Processing helix chain 'A' and resid 972 through 978 Processing helix chain 'A' and resid 983 through 991 removed outlier: 3.767A pdb=" N PHE A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 999 No H-bonds generated for 'chain 'A' and resid 997 through 999' Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 3.862A pdb=" N LEU A1010 " --> pdb=" O TYR A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1043 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 3.517A pdb=" N ALA A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 3.882A pdb=" N ILE A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1137 removed outlier: 3.895A pdb=" N SER A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Proline residue: A1126 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 155 through 157 removed outlier: 3.678A pdb=" N GLY A 350 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 354 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 255 through 257 Processing sheet with id= C, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.957A pdb=" N ASP A 287 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 299 through 303 Processing sheet with id= E, first strand: chain 'A' and resid 769 through 772 removed outlier: 6.746A pdb=" N VAL A 895 " --> pdb=" O CYS A 879 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY A 881 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 897 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 913 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 523 through 526 removed outlier: 6.873A pdb=" N GLY A 747 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A 518 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 745 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU A 520 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N LEU A 743 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE A 697 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 745 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 695 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY A 747 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG A 693 " --> pdb=" O GLY A 747 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 659 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 648 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG A 652 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 634 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 580 through 582 Processing sheet with id= H, first strand: chain 'A' and resid 824 through 826 Processing sheet with id= I, first strand: chain 'A' and resid 610 through 614 removed outlier: 4.061A pdb=" N LEU A 622 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 918 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: 2.56 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: 1.22 - 1.34: 2340 1.34 - 1.46: 1548 1.46 - 1.58: 3592 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 7541 Sorted by residual: bond pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.684 1.782 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" F4 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.686 1.782 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.778 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" N PRO A 285 " pdb=" CD PRO A 285 " ideal model delta sigma weight residual 1.473 1.443 0.030 1.40e-02 5.10e+03 4.49e+00 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 89.14 - 107.21: 196 107.21 - 125.28: 9925 125.28 - 143.35: 102 143.35 - 161.42: 0 161.42 - 179.49: 2 Bond angle restraints: 10225 Sorted by residual: angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F2 ALF A1201 " ideal model delta sigma weight residual 108.68 179.49 -70.81 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.63 178.84 -69.21 3.00e+00 1.11e-01 5.32e+02 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 110.21 89.14 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.69 89.92 19.77 3.00e+00 1.11e-01 4.34e+01 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.59 90.28 19.31 3.00e+00 1.11e-01 4.14e+01 ... (remaining 10220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4104 17.74 - 35.47: 343 35.47 - 53.20: 58 53.20 - 70.94: 11 70.94 - 88.67: 9 Dihedral angle restraints: 4525 sinusoidal: 1792 harmonic: 2733 Sorted by residual: dihedral pdb=" CA TRP A 369 " pdb=" C TRP A 369 " pdb=" N ALA A 370 " pdb=" CA ALA A 370 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA THR A 582 " pdb=" C THR A 582 " pdb=" N PHE A 583 " pdb=" CA PHE A 583 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR A 979 " pdb=" C THR A 979 " pdb=" N CYS A 980 " pdb=" CA CYS A 980 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 751 0.039 - 0.077: 330 0.077 - 0.116: 104 0.116 - 0.155: 21 0.155 - 0.193: 5 Chirality restraints: 1211 Sorted by residual: chirality pdb=" CA GLU A 237 " pdb=" N GLU A 237 " pdb=" C GLU A 237 " pdb=" CB GLU A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CB ILE A 334 " pdb=" CA ILE A 334 " pdb=" CG1 ILE A 334 " pdb=" CG2 ILE A 334 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1208 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 158 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 159 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 360 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 361 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 858 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 859 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 859 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 859 " 0.026 5.00e-02 4.00e+02 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 5239 3.10 - 3.70: 11469 3.70 - 4.30: 16655 4.30 - 4.90: 27665 Nonbonded interactions: 61084 Sorted by model distance: nonbonded pdb=" O PHE A1102 " pdb=" OD1 ASP A1103 " model vdw 1.902 3.040 nonbonded pdb=" O ASP A 882 " pdb="MG MG A1202 " model vdw 2.128 2.170 nonbonded pdb=" OD1 ASN A 885 " pdb="MG MG A1202 " model vdw 2.130 2.170 nonbonded pdb=" O ASP A1100 " pdb=" OD1 ASP A1100 " model vdw 2.137 3.040 nonbonded pdb=" OG SER A 594 " pdb=" OD1 ASP A 596 " model vdw 2.241 2.440 ... (remaining 61079 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 5.040 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 7541 Z= 0.286 Angle : 1.331 70.809 10225 Z= 0.564 Chirality : 0.048 0.193 1211 Planarity : 0.005 0.112 1267 Dihedral : 13.974 88.675 2755 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.78 (0.27), residues: 919 helix: -0.41 (0.24), residues: 419 sheet: -1.74 (0.42), residues: 150 loop : -1.72 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 660 HIS 0.008 0.001 HIS A 945 PHE 0.014 0.002 PHE A 843 TYR 0.025 0.002 TYR A 198 ARG 0.017 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.814 Fit side-chains REVERT: A 516 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8193 (ttpp) REVERT: A 795 GLN cc_start: 0.8370 (tt0) cc_final: 0.7985 (tt0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1659 time to fit residues: 26.0206 Evaluate side-chains 92 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.183 Angle : 0.878 31.928 10225 Z= 0.374 Chirality : 0.042 0.143 1211 Planarity : 0.004 0.070 1267 Dihedral : 4.932 23.390 1004 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.60 % Allowed : 8.08 % Favored : 91.31 % 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: -1.43 (0.28), residues: 919 helix: 0.02 (0.25), residues: 422 sheet: -1.69 (0.42), residues: 151 loop : -1.68 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 369 HIS 0.006 0.001 HIS A 945 PHE 0.032 0.001 PHE A 202 TYR 0.018 0.001 TYR A 707 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.872 Fit side-chains REVERT: A 795 GLN cc_start: 0.8374 (tt0) cc_final: 0.8068 (tt0) REVERT: A 1108 THR cc_start: 0.7774 (p) cc_final: 0.7492 (p) outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 0.1702 time to fit residues: 24.8917 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.170 Angle : 0.858 30.416 10225 Z= 0.361 Chirality : 0.041 0.139 1211 Planarity : 0.004 0.046 1267 Dihedral : 4.681 23.122 1004 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.97 % Allowed : 11.10 % Favored : 87.94 % 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: -1.21 (0.28), residues: 919 helix: 0.25 (0.25), residues: 421 sheet: -1.56 (0.42), residues: 151 loop : -1.66 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.007 0.001 HIS A 945 PHE 0.025 0.001 PHE A 202 TYR 0.024 0.001 TYR A 707 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.867 Fit side-chains REVERT: A 795 GLN cc_start: 0.8385 (tt0) cc_final: 0.8140 (tt0) REVERT: A 1108 THR cc_start: 0.7885 (p) cc_final: 0.7646 (p) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.1569 time to fit residues: 23.1775 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7541 Z= 0.419 Angle : 0.983 33.772 10225 Z= 0.438 Chirality : 0.048 0.169 1211 Planarity : 0.005 0.045 1267 Dihedral : 5.412 28.618 1004 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.69 % Allowed : 12.30 % Favored : 86.01 % 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: -1.80 (0.27), residues: 919 helix: -0.47 (0.24), residues: 423 sheet: -1.89 (0.40), residues: 158 loop : -1.58 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.010 0.001 HIS A 945 PHE 0.026 0.002 PHE A 202 TYR 0.023 0.002 TYR A 707 ARG 0.006 0.001 ARG A 946 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.828 Fit side-chains REVERT: A 223 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 277 LYS cc_start: 0.8161 (tttt) cc_final: 0.7953 (ttmt) REVERT: A 662 MET cc_start: 0.6781 (mtt) cc_final: 0.6457 (mtt) REVERT: A 690 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7565 (mm-30) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.2020 time to fit residues: 29.1860 Evaluate side-chains 100 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 1 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.165 Angle : 0.862 30.228 10225 Z= 0.365 Chirality : 0.041 0.156 1211 Planarity : 0.003 0.045 1267 Dihedral : 4.832 24.374 1004 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.81 % Allowed : 13.63 % Favored : 84.56 % 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: -1.21 (0.28), residues: 919 helix: 0.25 (0.26), residues: 419 sheet: -1.61 (0.42), residues: 145 loop : -1.63 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.005 0.001 HIS A 945 PHE 0.034 0.001 PHE A 202 TYR 0.026 0.001 TYR A 707 ARG 0.005 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.827 Fit side-chains REVERT: A 223 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7570 (mp) REVERT: A 690 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7392 (mm-30) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.1750 time to fit residues: 25.1162 Evaluate side-chains 100 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 47 optimal weight: 10.0000 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7541 Z= 0.146 Angle : 0.843 29.967 10225 Z= 0.352 Chirality : 0.040 0.150 1211 Planarity : 0.003 0.044 1267 Dihedral : 4.507 22.724 1004 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.29 % Allowed : 13.75 % Favored : 83.96 % 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: -0.98 (0.28), residues: 919 helix: 0.49 (0.26), residues: 419 sheet: -1.47 (0.42), residues: 145 loop : -1.59 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.005 0.001 HIS A 945 PHE 0.031 0.001 PHE A 202 TYR 0.017 0.001 TYR A 707 ARG 0.005 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.844 Fit side-chains REVERT: A 223 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 568 ASP cc_start: 0.7294 (t0) cc_final: 0.7017 (t0) REVERT: A 662 MET cc_start: 0.6548 (mtt) cc_final: 0.6330 (mtt) REVERT: A 939 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6726 (tt) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1616 time to fit residues: 25.9325 Evaluate side-chains 99 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1083 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.220 Angle : 0.880 30.724 10225 Z= 0.375 Chirality : 0.043 0.274 1211 Planarity : 0.004 0.044 1267 Dihedral : 4.690 24.706 1004 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.29 % Allowed : 14.72 % Favored : 82.99 % 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: -1.12 (0.28), residues: 919 helix: 0.27 (0.26), residues: 419 sheet: -1.51 (0.42), residues: 145 loop : -1.52 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 369 HIS 0.007 0.001 HIS A 945 PHE 0.032 0.002 PHE A 987 TYR 0.018 0.001 TYR A 707 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.820 Fit side-chains REVERT: A 223 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 362 LEU cc_start: 0.5984 (mt) cc_final: 0.5720 (mt) REVERT: A 939 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6932 (tt) outliers start: 19 outliers final: 15 residues processed: 108 average time/residue: 0.1703 time to fit residues: 26.0580 Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1079 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7541 Z= 0.154 Angle : 0.853 30.036 10225 Z= 0.358 Chirality : 0.041 0.145 1211 Planarity : 0.003 0.044 1267 Dihedral : 4.522 22.861 1004 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.41 % Allowed : 14.96 % Favored : 82.63 % 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: -0.96 (0.28), residues: 919 helix: 0.43 (0.26), residues: 419 sheet: -1.43 (0.42), residues: 145 loop : -1.50 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.005 0.001 HIS A 945 PHE 0.033 0.001 PHE A 202 TYR 0.018 0.001 TYR A 632 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.906 Fit side-chains REVERT: A 223 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7595 (mp) REVERT: A 362 LEU cc_start: 0.5890 (mt) cc_final: 0.5636 (mt) REVERT: A 939 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6668 (tt) outliers start: 20 outliers final: 16 residues processed: 107 average time/residue: 0.1675 time to fit residues: 25.8115 Evaluate side-chains 107 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1083 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.195 Angle : 0.869 30.358 10225 Z= 0.368 Chirality : 0.042 0.180 1211 Planarity : 0.004 0.044 1267 Dihedral : 4.625 24.305 1004 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.29 % Allowed : 15.56 % Favored : 82.15 % 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: -1.02 (0.28), residues: 919 helix: 0.33 (0.26), residues: 418 sheet: -1.45 (0.42), residues: 145 loop : -1.46 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.006 0.001 HIS A 945 PHE 0.031 0.002 PHE A 202 TYR 0.019 0.001 TYR A 632 ARG 0.002 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.815 Fit side-chains REVERT: A 223 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 362 LEU cc_start: 0.5893 (mt) cc_final: 0.5645 (mt) REVERT: A 939 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6845 (tt) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.1808 time to fit residues: 25.8996 Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1083 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.177 Angle : 0.863 30.241 10225 Z= 0.365 Chirality : 0.042 0.174 1211 Planarity : 0.003 0.045 1267 Dihedral : 4.574 23.419 1004 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.29 % Allowed : 15.68 % Favored : 82.03 % 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: -0.97 (0.28), residues: 919 helix: 0.40 (0.26), residues: 419 sheet: -1.42 (0.42), residues: 145 loop : -1.46 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 369 HIS 0.005 0.001 HIS A 945 PHE 0.034 0.001 PHE A 202 TYR 0.018 0.001 TYR A 632 ARG 0.003 0.000 ARG A 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.839 Fit side-chains REVERT: A 223 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7637 (mp) REVERT: A 362 LEU cc_start: 0.5892 (mt) cc_final: 0.5646 (mt) REVERT: A 833 MET cc_start: 0.5053 (tpp) cc_final: 0.4818 (tpp) REVERT: A 939 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6751 (tt) outliers start: 19 outliers final: 17 residues processed: 105 average time/residue: 0.1768 time to fit residues: 26.3297 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1083 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** 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 = 0.4283 r_free = 0.4283 target = 0.182467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146360 restraints weight = 7842.579| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.95 r_work: 0.3818 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.170 Angle : 0.861 30.182 10225 Z= 0.363 Chirality : 0.041 0.159 1211 Planarity : 0.003 0.044 1267 Dihedral : 4.539 23.395 1004 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.29 % Allowed : 15.92 % Favored : 81.79 % 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: -0.93 (0.28), residues: 919 helix: 0.46 (0.26), residues: 419 sheet: -1.40 (0.42), residues: 145 loop : -1.48 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.005 0.001 HIS A 945 PHE 0.035 0.001 PHE A 202 TYR 0.018 0.001 TYR A 632 ARG 0.003 0.000 ARG A 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.64 seconds wall clock time: 35 minutes 21.57 seconds (2121.57 seconds total)